Thursday, November 30, 2006

Post-Christian Europe, part II   posted by Razib @ 11/30/2006 10:44:00 PM

My post about Post-Christian Europe attracted several responses. Below I took the data from the chart rank ordering by belief in God. You note that as belief in God decreases, lack of belief in God or a Spirit increases as well, but belief in Spirit increases to a greater extent than lack of any belief at all.

Here is data from the least God-believing nation in the EU, Estonia,

Q: What religion is the dearest, most cherished for you?

* Lutheran 39%
* Orthodox 28%
* Roman Catholic 10%
* Taara Religion 6%
* Estonian Indigenous Religion/Estonian Native Religion 5%
* Baptist 5%
* Buddhism 4%
* Jehovah's Witnesses 3%
* Pentecostalists 3%
* Old Believers 2%
* Hinduism 1%
* Mormonism 1%
* Islam less than 1%
* Other 4%
* None 19%

Note that 11% of Estonians are now explicit Neo-Pagans.

At Blogs for Bush Mark Noonan states:
Europeans aren't having children. Without the impetus of belief in a definitive God who rules the universe, having children just becomes an expensive nusiance. Most European countries are suffering net loss in population - save for those countries which continue to allow mass immigration from Arab nations.

This is a common opinion. Secular European societies are dying. But this avoids an interesting point. There isn't much of a correlation between European societies for birthrate and God belief. I acknowledge that within societies there is probably a positive correlation between religiosity and fecundity (aside from a few exceptions like South Korea, where greater religiosity predicts higher socioeconomic status), but as you note below there is a rather flat trendline, and that is birthrate normalized to the modal value (Ireland). Here are the values for the United States....

"Which of the following statements comes closest to your belief about God: you believe in God; you don't believe in God, but you believe in some other universal spirit or higher power; or you don't believe in either?"

God: 82%
Spirit: 9%
Neither: 8%
Unsure: 1%

Wednesday, November 29, 2006

Beyond Belief 2006 - a highlight   posted by Razib @ 11/29/2006 11:05:00 PM

Been watching Beyond Belief 2006. Funniest moment so far, V.S. Ramachandran recounts the % of people in a survey who considered themselves "above average" in intelligence. Take a guess. Answer below the fold.

98% of people surveyed (representative survey mind you!) considered themselves above average in intelligence.

Snatch culture   posted by Razib @ 11/29/2006 10:33:00 PM

Yesterday there was an interview with an author of a book about the rise of "raunch culture" among today's youth on NPR. By coincidence yesterday was also the day that Britney Spears flashed her beaver to the world. Now, you might think that Spears isn't the sharpest tool in the shed, that she couldn't anticipate that running around without underwear, wearing a skirt, and mugging for the paparazzi, would inevitably lead to some labial exposure. Oops, she did it again! Cultural weapons of mass destruction indeed. And I laughed when K-Fed asked for custody....

Update: Britney bares anus!

The Black-White IQ Gap: Is It Closing? Will It Ever Go Away?   posted by Razib @ 11/29/2006 10:13:00 PM

Update: video, audio and PDFs available

Charles Murray emailed me a notice for this today, so for those in the D.C. area:

Start: Tuesday, November 28, 2006 10:00 AM
End: Tuesday, November 28, 2006 12:00 PM
Location: Wohlstetter Conference Center, Twelfth Floor, AEI 1150 Seventeenth Street, N.W., Washington, D.C. 20036

For decades, the difference in the test scores of blacks and whites on the SAT, National Assessment of Educational Progress test, Armed Forces Qualification Test, and traditional IQ tests has been a vexed issue for American educational policy. Two of the leading scholars of this controversial topic, James R. Flynn of the University of Otago (New Zealand) and Charles Murray of AEI, will debate the causes of the difference, its implications, and recent trends. New studies of the subject by Professor Flynn and by Mr. Murray will be available for distribution at the session.


James R. Flynn, University of Otago
Charles Murray, AEI

Spore: The Video Game That Creationists Will Hate   posted by TangoMan @ 11/29/2006 03:27:00 PM

Will Wright of The Sims and SimCity fame has been developing his new game Spore for over 6 years and the canvas he's painting on is large indeed for the game begins with the player controlling the evolution of cells within a tidal pool and it progresses up the evolutionary ladder, with intermediate stops at controlling individual creatures which have evolved from the cells, controlling early tribes of creatures, controlling the sociological aspects of creatures living in cities, controlling civilizational issues confronting the creatures, and finally leading the creatures into a space-based expansion where they meet other species that have evolved from different evolutionary niches.

Wikipedia has an extensive write-up on the entire project and notes that Wright is using procedural generation code to allow the player to define their evolutionary features via permutations rather than simply drawing the features from preexisting code.

To illustrate the the power of evolutionary branching that permeates the game consider the following:

The Cell Phase is the starting point of the game. The player guides a simple micro-organism (microbe) around in a 2D environment, eating other, weaker cells. There are at least three other types of cells, two of which can eat the player's microbe to begin with. Once the microbe has eaten several cells, it lays an egg which, when clicked, opens the creature editor which allows the player to modify the appearance, shape, and abilities of the microbe. This includes adding offensive abilities. For example, in Will Wright's 2005 demo, he added a small spike which allows the player's microbe to attack the organisms which would previously eat the player's microbe. Each time the player's microbe progresses to the next generation, it grows larger. Once the microbe grows to a certain size, the player leaves the 2D world of the microscopic and enters the creature phase.

Spore seems to be generating quite a bit of buzz and anticipation within the gaming community and I imagine that kids who are playing the game and seeing evolution play out before their eyes will come to understand the evolution vs. creationism debate with a deeper understanding of the process underlying evolution. The upshot here: the more entertaining the lesson the greater its impact.

Schizophrenia and IQ   posted by p-ter @ 11/29/2006 02:17:00 PM

Low IQ is a risk factor for developing schizophrenia, though the mechanism behind this association is somewhat unclear. A new study sheds a little light on this subject, and suggests the link might be genetic. The gene in questions is neuregulin 1, about which little is known. They find, first, that a regulatory SNP is associated with the development of psychotic symptoms in a particularly at-risk population (see part a above-- each bar is the percentage of subjects developing symptoms for a given genotype). They also find lower levels of activity in certain part of the brain in the patients with the TT genotype (see parts b and c above).

Further, here are the means and standard deviations of the IQ distributions of the different genotypes:

CC: 101.9 (8.4)
CT: 100.4 (9.4)
TT: 94.3 (6.9)

So this regulatory polymorphism could explain some of the natural variation in IQ.

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Tuesday, November 28, 2006

Post-Christian, but not secular, Europe   posted by Razib @ 11/28/2006 10:13:00 PM

From page 11 of a European Commission survey....

"Wrong door" raids   posted by amnestic @ 11/28/2006 04:27:00 PM

The Agitator is doing a fine job on the play-by-play following the Kathryn Johnston shooting. These are your drug war tax dollars at work. For a weak-willed waffler like myself it is nice to come across a policy area where the side of reason and justice is so obvious. Rapidly approaching single issue voter status.
By conservative estimates, there are about 110 of these types of raids per day in America. The vast majority are for drug crimes. Think this was the only one conducted after shoddy police work? Think this was the only one conducted based solely on the word of an informant? Think it's pure coincidence that in the one raid that made national attention last week, we now learn that something went severely wrong in the investigation that led to it?

Of course not. This is standard operating procedure. This the way it's done in a huge number of jurisdictions across the country. Not all. But far too many. I've had police officers tell me raids are never launched based solely on the word of an informant. But this one was. I've had police officers tell me there's always extensive corroborating investigation to verify the address, house, and suspect. But not this time. I've had police officers tell me paramilitary raids are only conducted with the suspect is extremely dangerous, and has a history of violent behavior. Not this time. I've had police officers tell me they only target big suppliers with these raids, not small-time dealers or users. Again -- that wasn't the case, here.

I find it hard to believe that the only time time these shortcuts have been used are in those raids we read about in the newspaper -- where an innocent person dies.

These assaults on people's homes are high-stakes and have an extremely thin margin for error. Couple that with the inherent shortcomings of relying on shady informants -- a critical tool in drug policing -- and you get a recipe for hundreds of innocent people wrongly terrorized, and dozens more who end up dead. By my count, Kathryn Johnston is number 41. Throw in nonviolent offenders and she's number 61 -- at least (I'm sure I haven't found all of those cases).

And all of this -- for what?

To stop people from getting high.

Genomics vs Insurance   posted by amnestic @ 11/28/2006 12:11:00 PM

Free Exchange has a comment on a comment on an article about the ability of genomics-informed medicine to break the game of chance at the very core of the insurance industry. The analogy to learning not to build houses in natural disaster areas is made, but with certain diseases no prevention (post-natally) is possible.

An interesting point though re: insuring the poor. Probably you've all thought of it this way before:
But what about the poor? It is hard to see any reason why insurance companies should subsidize them. If society thinks that poor families should have insurance, then society should pay for it through the tax code, not slap regulations on insurance companies to keep information from reaching the market.

In a related note, there is a Google Techtalk available featuring Russ B. Altman, the guy heading PharmGKB, an ambitious project to link SNPs to pharmacological outcomes. As a for instance, something like 7% of people have SNPs that disable the enzyme that turns codeine into morphine, so they get no pain relief from Tylenol 3. So let's not waste the insurance money buying them that medication.

If you like watching videos of people being cool on the internet, you might also want to check out TEDTalks. In one of my favorites, Dr. Robert Fischell shoots magnet guns at peoples' heads and disrupts migraines before they start.

Monday, November 27, 2006

Tonegawa   posted by amnestic @ 11/27/2006 09:50:00 PM

Are bloggers more like sharks in a feeding frenzy or vultures on deadmeat?

See the populist rally the mob:

Ah... the Perfumed Class. Our Lords and Masters, the Principle Investigator Princes wandering over their incandescent domains, bestowing upon their peasant postdocs, their servile grad students, their precious beneficence... Don't you love them?
In summary, I am sorry, but I have to say to you that at present and under the present circumstances, I do not feel comfortable at all to have you here as a junior faculty colleague.
Step off Logan Airport, and I'll dip you in tempura batter, fry you in peanut oil and eat you for dinner.

I love that he is able to riff off of Tonegawa's ethnicity with such dexterity.

Oh and here's one who was even more clever with Tonegawa's name. See how she replaced Tone with Toady! So CLEVER! Wish I could pat her on the head for it. "I like to think he was strong-armed into stepping down."

Let's do something besides join the dogpile.

Tonegawa won the Nobel Prize in 1987.

Susumu Tonegawa was the one who finally answered the question how the gene material in B cells could suffice to create the structures of a seemingly endless number of different antibodies. In 1976 he could in a convincing and elegant manner show how different immunoglobulin genes which were far apart in the embryonic cell in the B lymphocyte had been moved in closer contact. Under development from the germ cells (the sperm and egg cell) to an antibody producing B lymphocyte the genes forming the immunoglobulins had accordingly been redistributed. In subsequent experiment Tonegawa could clarify how different pieces of the genome were moved around, recombined and even could be "lost" to finally give rise to the DNA which is found in the mature B lymphocyte.

Since then he has been a leader in the development of transgenic technologies:

Using the phage P1-derived Cre/loxP recombination system, we have developed a method to create mice in which the deletion (knockout) of virtually any gene of interest is restricted to a subregion or a specific cell type in the brain such as the pyramidal cells of the hippocampal CA1 region. The Cre/loxP recombination–based gene deletion appears to require a certain level of Cre protein expression. The brain subregional restricted gene knockout should allow a more precise analysis of the impact of a gene mutation on animal behaviors.

These technologies have become indispensable in the study of memory. You can knockout whatever gene you want in just the portion of the brain circuitry that theory has pointed to as important. One of the first (if not the first) applications was the production of mice lacking NMDA-type glutamate receptors in the CA1 region of the hippocampus. The casual reader or layperson can basically equate NMDA receptors with synaptic plasticity, meaning the changes in neural transmission that underlie memory. These CA1-NMDAR KO mice suck at memory.

But Tonegawa also provides a refined behavioral and theoretical approach. The hippocampus has a strong flow of connectivity from area DG to CA3 to CA1. CA3 has highly recurrent connections and thus has been modeled as a pattern completion module. Knocking out CA3 NMDA receptors doesn't have an obvious effect on memory like the CA1 version. Instead, one has to dig and understand clearly the role of different hippocampal subregions to find the CA3-KOs' specific deficit.

Pattern completion, the ability to retrieve complete memories on the basis of incomplete sets of cues, is a crucial function of biological memory systems. The extensive recurrent connectivity of the CA3 area of hippocampus has led to suggestions that it might provide this function. We have tested this hypothesis by generating and analyzing a genetically engineered mouse strain in which the N-methyl-D-asparate (NMDA) receptor gene is ablated specifically in the CA3 pyramidal cells of adult mice. The mutant mice normally acquired and retrieved spatial reference memory in the Morris water maze, but they were impaired in retrieving this memory when presented with a fraction of the original cues. Similarly, hippocampal CA1 pyramidal cells in mutant mice displayed normal place-related activity in a full-cue environment but showed a reduction in activity upon partial cue removal. These results provide direct evidence for CA3 NMDA receptor involvement in associative memory recall.

More recently Tonegawa and colleagues have emphasized the role of regulation of protein synthesis in memory storage, showing that certain pathways many equate with regulation at the level of mRNA synthesis (transcription) also regulate translation factors directly. This short circuits the loop. There is no need for a signal to travel from synapse to nucleus and back in order to make changes in the structure of a synapse. The same group has provided a unique theoretical insight in developing the clustered plasticity model in which changes involved in memory storage are coordinated at neighboring synapses.

The papers in the Arc-stravaganza a couple weeks ago all cited Tonegawa (and other very important PI's: Sur and Majewska) as early empirical evidence that Arc plays a role in reducing noise in synaptic plasticity rather than directly increasing the strength of "signal" synapses as many predicted.

Just some light reading in case you get tired of too much cleverness. As I mentioned at Shelley's blog, I think the peanut gallery could stand to quiet down some until they understand in technical detail the degree to which Karpova and Tonegawa were trying to achieve the same technology. I also agree with the original ad hoc report that we shouldn't be privy to those emails. Unfortunately, we are privy because of some highly unprofessional and noncollegial media wagging performed by somebody besides our latest burning patriarchy effigy.

Addling the Brain   posted by David Boxenhorn @ 11/27/2006 11:36:00 AM

A few days ago, I came across a very interesting article on lexical-gustatory synaesthesia (via Language Hat):

Lexical-gustatories involuntarily “taste” words when they hear them, or even try to recall them, she wrote in a study, “Words on the Tip of the Tongue,” published in the issue of Nature dated Thursday. She has found only 10 such people in Europe and the United States.

Magnetic-resonance imaging indicates that they are not faking, she said. The correct words light up the taste regions of their brains. Also, when given a surprise test a year later, they taste the same foods on hearing the words again.

(Synaesthetes are hardly ever described as “suffering from” the syndrome, because their doubled perceptions excite envy in many of us mere sensual Muggles.)

It can be unpleasant, however. One subject, Dr. Simner said, hates driving, because the road signs flood his mouth with everything from pistachio ice cream to ear wax.

Now Amnestic points me to a fascinating video of V.S. Ramachandran talking about the subject. Some reactions to the video:

1. So synaesthesia is was LSD users report!
2. Synaesthesia can be good for something - e.g. patterns jump out at you
3. Einstein might have had some type of synaesthesia
4. I can easily see how some kind of synaesthesia could give rise to new "modules" - e.g. a prime number identifier

One of the most interesting things about the Language Hat link was that quite a few synaesthetes, of various kinds, showed up to share their perceptions. I was wondering if any GNXP readers had something to share? In particular, I am interested in ways synaesthesia is good (or bad) for you.

UPDATE: This sounds like some kind of synaesthesia:

"Squaring numbers is a symmetrical process that I like very much," he says. "And when I divide one number by another, say, 13 divided by 97, I see a spiral rotating downwards in larger and larger loops that seem to warp and curve. The shapes coalesce into the right number. I never write anything down."
His mathematical abilities are so extraordinary that it took a long time for them to be recognised. Daniel struggled at school (why, he wondered, were the numbers in the textbook not printed in their true colours, nine in blue, and so on?). He got a B at Maths GCSE. He wasn't diagnosed with Asperger's syndrome until three years ago, at 25. Sooner would have been better "both for me and my parents"; consciousness-raising is part of his motivation for writing his book. "My condition is invisible otherwise."

Scientists at California's Center for Brain Studies were astounded when, two years ago, they discovered his facility for discerning prime numbers. They had assumed he must have been trained to do it. But to him, it is more like an instinctive process: "Prime numbers feel smooth, like pebbles".

Genetics and engineering   posted by the @ 11/27/2006 12:45:00 AM

Wanted: Biologists who can speak 'math,' engineers fluent in genetics

Biologists, computer scientists and engineers speak different languages: Mention "vector" to a molecular biologist and a plasmid (a circular piece of bacterial DNA used in gene cloning) comes to mind. Say "vector" to an engineer, and she thinks of a mathematical concept. Similarly with "expression": To a biologist, it means protein production from a gene; to an engineer, it's an equation.

Cute, but there's discussion of more serious topics.

Lidstrom, who conducts an elective biology class for engineers, has found that biologists are motivated by the "what," while engineers are motivated by the "how." She told a room packed with MIT students and faculty that "engineering students tend to view biology as magic because they don't see us using differential equations. And often they don't even necessarily want to understand the 'what' of biology--they just want to use it.

I'm not sure that helpfully describes the situation, but there's a more interesting question. How do you teach engineers biology (esp. genetics)? The undergrad classes run out of Lewis-Sigler at Princeton seem like a good move in the opposite direction: training natural scientists in quantitative thinking.

Sunday, November 26, 2006

Beyond Belief 2006   posted by Razib @ 11/26/2006 12:49:00 PM

Chris of Mixing Memory points me to Beyond Belief 2006, which is about "Science, Religion, Reason and Survival" (videos viewable online!) As Chris notes the list is heavily weighted toward scientists who don't study religion and seem to be offering their own personal opinions. Ann Dryan seems to be aging gracefully.

From Today's Papers   posted by DavidB @ 11/26/2006 01:26:00 AM

A few items of interest from today's British newspapers:

The lead story in the Sunday Telegraph reports that a majority of people in both England and Scotland want independence from each other. But I don't think it will happen, because it is against the vested interests of politicians and bureaucrats.

Also in the Telegraph, an article on the future of the Jewish community in Britain.

In the Sunday Times, a sensible article by Simon Jenkins on drugs policy. Of course, he is not quite right to say that the end of alcohol prohibition put Al Capone out of business: apart from the detail of whether Capone had already been busted for tax evasion, the end of Prohibition just meant that the crime organisations it had created turned to other sources of income, notably from drugs. But the principle is sound: legal prohibition of widely popular activities such as drugs, prostitution, or gambling is the raison d'etre of organised crime.

Added: The lead story in The Observer is a report that Tony Blair intends to make a sort-of-apology - expressing 'deep sorrow' - for Britain's involvement in the slave trade before abolishing it 200 years ago.

Enough with the apologies, already. Apart from the usual selectivity of such gestures - when are the French going to apologise for the Norman Conquest, I'd like to know - and the way they reinforce the tendency to victimology, the fundamental objection is to the idea of vicarious guilt for the actions of others. And I don't want that creeping Jesus Blair apologising on my behalf, let alone my distant ancestors'.

Also in the Observer, Jasper Gerard has some nice comments on the difficulty of finding 'moderate' Muslim spokespersons:

Like a famous Belgian, a moderate Muslim is devilishly elusive... Every time we anoint some cove the 'voice of moderation' he turns out quietly to favour female genital mutilation or a spot of light bombing.

Gerard also has a comment on Kate Moss's comedy turn for charity with Matt Lucas last week. But there seems to be a conflict of reports on the wording of Kate's best line. Some say it was 'I'll do anything for a bag of Quavers' (a popular snack), and others 'I'm anybody's for a bag of Quavers'. But Gerard has it as 'I'll give you a gob job for a bag of Quavers'. This has the ring of authenticity, but does anyone know the truth? Anyway, expect the sales of Quavers to rocket.

PS: in case anyone is wondering if I'll ever write anything about genes again, I have a series of posts about Sewall Wright in gestation, but these things take time.

Friday, November 24, 2006

I'd be fired if that were my job   posted by amnestic @ 11/24/2006 06:04:00 PM

I've been trying to come up with some clever way of framing the latest RNAi work in a mythological context, but I'm afraid it isn't lending itself all that well. You see, the family of final effector proteins for RNA-induced silencing are called Argonautes. Why did they name them Argonautes and then fall off on their Apollonisian naming scheme? Beats me, but they are really going haywire now. They named one of the argonaute proteins Caesar!

In this report from Yigit et al., they knocked out every Argonaute family member in C. elegans, the lovely translucent worm genetic model system. You'd think there would be a tie-in there. The preview about the report is titled "Knocking out the Argonautes," but alas, the only knocking out I can discover involves Circe and the Odyssey cats. The worm has a rather different system for RNAi than we do. The focus of this paper was a whole class of Argonautes that worms have that there isn't a human or even drosophila homologue for. They are called SAGOs (say-go) for Synthetic secondary-siRNA ArGOnautes.

One of the purposes of RNAi is to defend against viral infection by using chopped up viral genomes as templates for small RNAs to load into RNA chomping or sequestering machines. In worms, this system is referred to as the exo-RNAi system. In the model proposed by Yigit et al., Worms differ from many other organisms in that they carry out their defensive mission in two steps. In step one, a primary the viral dsRNA is chopped up to produce template a fewsmall RNAs from both strands. These are loaded into a Primary Argonaute-containing silencing complex. When this complex chops up its targets it also happens to trigger an production of new small RNAs based off of the sequence upstream of its target sequence in the viral RNA. These are the secondary siRNAs. In step 2, a Secondary Argonaute (SAGO) complex is loaded with these secondary siRNAs. The SAGOs don't have the ability to cleave RNAs. They can only bind them and perhaps drag them to some RNA degradation center or other.

Things I learned from this paper and the associated preview include: You can predict whether an Argonaute protein will have RNA cleavage activity based on the conservation of three amino acid residues (two aspartic acids and a hisitidine); in an uncommon twist, humans actually have less of a protein class than other organisms, 8 AGOs as opposed to 27 in worms and 10 in mustard plants (flies have 5, so we are still superior to flies), ~50 in the Argonautika; multiple RNAi (endo- and exo-) pathways feed into the second (SAGO) step in the worm such that the availability of SAGOs can be a limiting factor, and increasing or decreasing the activity of one of the competing pathways can affect the efficiency of the other; worms have an endo-RNAi pathway that is somehow distinguishable from their miRNA pathway, though I'm not sure what the distinction is just yet. My understanding was that I could call endogenously produced small interfering RNAs microRNAs. From their model, it looks like the endo-RNAi pathway is involved in transcription-level silencing (i.e. heterochromatin formation). Probably endo-siRNAs don't go through the stereotyped pri-, pre-, mature steps that miRNAs do.

Jason and the Argonauts is on in an hour on Turner Classic Movies. The only correspondence I can think of is maybe to refer to the primary Argonaute as Heracles, since he was only there for the first part of the adventure, after which he just hung out on an island cos he was all sad that the nymphs stole his boy-toy. I dunno if that's in the movie or not. Something tells me no.

Thursday, November 23, 2006

Breaking the fast   posted by DavidB @ 11/23/2006 05:32:00 AM

Not a genetic story, but amusing (well, I thought so), this report from today's London Times:

A Muslim who killed a swan [a protected species] during Ramadan has been given a two-month prison sentence. Shamsu Miah, 52, killed the mute swan at a boating pond in Llandudno, North Wales, on September 25. When challenged by police he said: "I am a Muslim. I am fasting. I needed to eat." Llandudno magistrates were told that Miah, from the town, had white feathers stuck in his beard and blood on his shirt.

Which raises the questions: did he actually eat it raw? And was this halal?

Dawkins on In Our Time   posted by Razib @ 11/23/2006 04:56:00 AM

Richard Dawkins will be on In Our Time to discuss the evolutionary origins of altruism. They are pretty good about getting the archive up in a day or so. Interesting that they illustrate the idea with Mr. a priori Kant, or am I being pretentious and misunderstanding Kant? I simply suspect that Dawkins will argue and elucidate an evolutionarily beneficial situationalism.

Wednesday, November 22, 2006

Happy Thanksgiving!   posted by Razib @ 11/22/2006 11:49:00 PM

Drunk thugz? Apparently Asians have the market on violin playing in Europe too....

Tangled Bank & Four Stone Hearth   posted by Razib @ 11/22/2006 09:26:00 PM

Biology and anthropology carnivals. Have a good Thanksgiving!

Neurotransmitters and vesicles   posted by amnestic @ 11/22/2006 06:06:00 PM

You know the names of some neurotransmitters: dopamine, serotonin, norepinephrine. Glutamate is the major excitatory neurotransmitter and GABA is the major inhibitory one, right?. All neurotransmitters function in a similar way to communicate between two neurons. The pre-synaptic neuron sends messages in the form of neurotransmitter for the post-synaptic neuron to receive at neurotransmitter receptors.

Let's focus on the pre-synaptic side for a minute. Neurotransmitters aren't released one at a time. They are released in bulk, thousands at once. This is achieved by packaging the neurotransmitters up into a little sac in the pre-synaptic termincal called a synaptic vesicle. You can see hundreds of these in electron micrographs of synapse.

When the pre-synaptic neuron gets the cue to dump neurotransmitters, the vesicle, which has a lipid bilayer membrane just like the cell's membrane, fuses with the cell membrane through an elaborate protein winching mechanism. This releases the entire vesicle contents into the synapse at once. This process isn't entirely understood, but many of the major proteins that interact between the cell membrane and the vesicle membrane are known. So a group recently did a ton of mass spec and quantitative measurements to determine more precisely the protein content of a given synaptic vesicle and produces a model vesicle. I think it is just lovely:

They found that a surpising amount of the membrane space on a vesicle was 'dedicated' meaning that it either contained a trans-membrane protein or certain lipid molecules that are unlikely to flow around very much within the membrane. Here is one of my favorite passages:

A picture is emerging in which the membrane resembles a cobblestone pavement, with the proteins organized in patches that are surrouneded by lipid rims, rather than icebergs floating in a sea of lipids.

The HapMap and copy number variation   posted by p-ter @ 11/22/2006 03:05:00 PM

In the HapMap database are genotypes for over 3 million single nucleotide polymorphisms (SNPs) in 270 people-- 90 people of Western European descent, 90 people from Nigeria, 45 from Japan, and 45 from China. This is a spectacular resource for all sorts of population genetic, medical, and evolutionary studies. Yet SNPs aren't the only way people vary-- duplications and deletions of genome material are also important (as are other changes). Now, for those same 270 people who make up the HapMap, a catalogue of the duplications and deletions (or really, all variation in copy number) segregating in the populations has been generated. This is reported in the most recent issue of Nature.

Of note, they find that the actual quantity of DNA affected by these copy number variants covers a full 12% (!) of the genome. That is a huge amount of variation (we're all genetically 99% the same, right?), but is it functional? The authors note that copy number changes tend to stay away from known genes, but there are a number of examples of functional copy number changes, including ones that influence succeptibility to the HIV virus or glomulonephritis (whatever that is). I expect these sorts of variants to be very important in complex traits-- they provide the raw material for subtle changes in regulatory networks, which will then affect subtle phenotypic changes.

Another interesting story is that of the MAPT locus. This locus is marked by an inversion on one haplotype that has been under selection in Europeans. The two haplotypes at the locus are extremely diverged, which to some suggest another introgression event from Neandertals. An inversion that remains polymorphic in a population is interesting, because individuals heterozygous for the inversion are expected to have reduced fertility (recombination in the area of the inversion leads to imbalanced chromosomes). The apparent positive selection on this locus is, in that context, a bit puzzling. I'm not sure the authors realize this, but they might have solved this problem--if the duplication is the cause of the increased fitness, it would conteract the deleterious effects of the inversion. Unfortunately, there's not a lot of detail here, and it's not even clear that the duplication is on the positively selected haplotype.

Finally, there seem be some copy number variants that are have very different frequencies in the populations examined, suggesting possible differential selection. Among them is the variant known to decrease succeptibility to HIV and another known to play a role in androgen metabolism.

So the HapMap cell lines pay off once again and the human genetics community reaps the rewards; it's hard to believe that a number of people were against the construction of this resource.

Tuesday, November 21, 2006

Europe and alcoholism   posted by Razib @ 11/21/2006 11:31:00 PM

Genetic Variability, Economic Behavior and the Formation of Social Norms: The Case of European Alcohol Consumption
Alcohol consumption patterns vary across Europe. Northern Europeans frequently engage in excessive drinking in social situations (EDSS), behavior less common in southern Europe. We develop a model to explore whether these behavioral differences could be rooted in genetic variations across Europe and then compounded by social reinforcement mechanisms. Our results suggest conditions exist in which EDSS can emerge as a strategy in a larger fraction of the population than is genetically predisposed to EDSS. Implications for the current effort to harmonize alcohol policy across the European Union are explored.

You can read the full working paper yourself. They don't seem to take into account superior southern European alcohol metabolization, but they do point out that northern Europeans are likely to be innately shyer. Alternative title: "Why Finns get shit-faced."

Science blogs that we're missing   posted by Razib @ 11/21/2006 08:55:00 PM

Open thread for links to science blogs of interest that aren't well known yet. Your own blog is fine too. I'll post the most interesting ones (to me) below the fold on an update to boost the pagerank for google.

Some blogs:

Phil Downey
Back Reaction
Agricultural Biodiversity

Update: Julian O'Dea.

"Eastern" vs. "Western" thinking   posted by Razib @ 11/21/2006 08:13:00 PM

Chris of Mixing Memory has a review of a paper which confirms the finding that East Asians think more holistically than Westerners. Specifically, East Asians often tend to look at context, while Westerners focus more specifically on the object of interest. In this case this model seemed to fall in light with the fact that East Asians, specifically Japanese, seemed to see wider web of repercussions for events, while Europeans tended to look at things in a more narrow frame, both temporally and in regards to social networks and what not. This is not a new field. Three years ago I reviewed Richard Nisbett's Geography of Thought, which made the same arguments based on the author's research. But, some qualifications need to be made: the paper above uses Japanese and Americans whites as exemplars of the two categories. Nisbett found an important geographical pattern: in terms of "analytic" vs. "holistic" thought, and a whole range of attitudes, English speaking cultures tended to be at one pole, and East Asians at another, with contintental Europeans in the middle. Additionally, most non-Europeans clustered with East Asians. This is important, because of course readers of this weblog will want to consider a possible innate genetic element to these cross-cultural differences. Obviously continent Europeans are not phylogenetically equidistant between East Asians and English speaking whites! Additionally, Nisbett found (and this is confirmed by Judith Richard Harris in No Two Alike) individuals of Asian ancestry raised in the United States clustered with other Americans, not with Asians. Significantly, individuals who arrived in North America (some subjects were Canadian, poor souls) during their teenage years from Asia (China) tended to exhibit cognitive styles which were hybridized between Western and Eastern modes. Finally, Nisbett found that citizens of Hong Kong (a former British colony) were particularly adept at "switching" between cognitive modes dependent on context, and, he found individuals from both cultures could be "trained" to think in the opposite mode relatively easily.

This is not to say that no differences in allele frequencies with behavior/cultural impact exist between the groups. Consider the variation in the frequency of DRD4 & MAOA across populations. But the differences are not, I suspect, going to be as easy as tallying up character differences between populations when cultural plasticity, along with wild cards like Toxoplasma gondii, are important components of the variance. Finally, I do have to wonder as to the popularity of analytic philosophy in the Anglo-American world, vs. "Continental" philosophy in places like France.

Haldane Papers   posted by DavidB @ 11/21/2006 04:57:00 AM

I think I once complained that there is no good collection of J. B. S. Haldane's technical papers in genetics (as distinct from his popular articles). If I did, I retract the complaint, as I find that there is already a very good collection: Selected genetics papers of J. B. S. Haldane, edited with an introduction by Krishna R. Dronamraju, Garland Publishing, NY, 1990. This is a big book (over 500 pages), containing most of Haldane's classic papers on the Mathematical Theory of Natural and Artificial Selection, and many others. Incidentally, it is sometimes said that these classic papers are 'reprinted' in an Appendix to Haldane's book The Causes of Evolution (1932), but this is hardly accurate. The Appendix contains only a brief summary of Haldane's main findings.

I must also retract another complaint. In a post on Haldane's Dilemma I said that there was a misprint in one of the formulae in Haldane's 1957 paper on the 'Cost of Natural Selection': a vital division stroke appeared to be omitted. I was therefore interested to see that in the reprint of the paper in Dronamraju's collection the division stroke is present where it should be. At first I thought that this must be an editorial correction, but this seemed odd because the reprint appeared to be a photographic copy. So I looked up the original printed version of the paper (in Journal of Genetics 1957), and found that the division stroke was there all along.

My error arose from relying on a pdf copy of Haldane's paper on the internet (see link in my earlier post). In the pdf file there is no trace whatever of the division stroke - not a single pixel - even at the highest magnification. So I am gratified to find that I was correct to find an error in the formula as it appeared in the pdf copy, but alarmed to find that a seemingly good pdf copy can be unreliable in this way. It is puzzling because other division strokes in the same paper have come out clearly enough.

This, I didn't believe....   posted by Razib @ 11/21/2006 12:21:00 AM

Some of you may know that I was not a self-aware atheist until the age of 8. Before that point I was nominally religious insofar as if someone asked I would have said I believed in God. If they asked what that meant I don't know what I would have said, it wasn't a question I considered. I had a vague Deist sense of God being the Ground of all Being, the Prime Mover, but I never really lived a life where a personal God was active. The religious instruction I received also indicated that there was an afterlife, a heaven. And a hell. And yet, today I just realized that despite these notional beliefs I held, between the ages of 4 and 6 I experienced a great deal of terror over the inevitability of death. I had specific ideas of bodies buried and decomposing and what not. During these bouts of terror I never even considered the possibility of an afterlife. These bouts abated as I grew older, and by the time I had my atheistic epiphany I wasn't concerned with the afterlife at all.

The only reason I recount this is to wonder: is it normal for children to have such a detailed fear of death? Or, do children normally accept the plausibility of life after death? I know from psychological studies that children seem to have an innate sense of ensoulment. I don't feel that I ever had this...I recall specifically fretting over bodily decomposition, and there was no awareness of "looking down" from the "outside." On the other hand children do hold in their mind many contradictory thoughts and ideas, just as adults do.

Monday, November 20, 2006

What is the minimal set?   posted by Razib @ 11/20/2006 09:06:00 PM

What are the minimal set of values for a Western nation-state?

Update: Aziz asks at Esmay's.

Mind Wars on Diane Rehm   posted by amnestic @ 11/20/2006 10:58:00 AM

Caught a little of Jonathan Moreno this morning. He's got a book out called Mind Wars that considers the implications of neuroscience research being funded by DARPA. Here and in another article I read he focuses on modafinil (branded as ProVigil) for USAF pilots. It's supposed to make you alert and cognitively unimpaired with less sleep. Sounds money to me. It is starting to be prescribed off-label to world travelers with jetlag.

When I saw a lecture about DARPA funded computational research to create smart battle robots, somebody asked about Asimov's rules for robots (i.e. don't harm humans). He was kind of laughed off. I think the possibility of robots that could have the type of volition that could back-fire on us is distant, is it something to ignore?

Another weird fantasy popped into my head while he was discussing remote-control. It seems like their might be an idea of giving soldiers neural implants. A nightmare future vision comes to mind of a captured soldier having his forcibly removed and badly patched. Speaking of remote control, check out wireless power.

Sunday, November 19, 2006

White eyes, gaze-detection, and sexiness   posted by agnostic @ 11/19/2006 01:55:00 PM

John Hawks comments on a new study suggesting that the reason human beings have white sclerae is to facilitate detection of what another person is looking at (press story here). Though the article is not out yet, the gist is that humans pay more attention to another person's eye movements, while other primates pay more attention to another's head movements in order to infer what the other is looking at. The pupil through which we look is only color-differentiated from the surrounding iris in people with light irises, but since the iris and pupil are concentric, if we could track the iris, we could track the pupil as well. And because our visual system is tuned to pick up on contrasts, especially between figure and background, a contrasting iris-sclera form would be ideal for tracking someone's eye direction. This in turn would have been useful in cooperative and learning situations where individuals need to focus on the same objects so that background information is shared, minimizing the need to spell out assumptions. This is similar to the Gricean Maxims in the linguistic field of pragmatics -- the more we share assumptions and follow cooperative norms, the less longwinded and lawyerly we have to be in communicating.

Some other thoughts, which may or may not be discussed by the authors:

1) Aside from detecting eye direction, a white sclera would also facilitate detecting emotional eye expressions, as the white sclera contrasts with the full range of human skin colors -- especially the darker ones, but even Irish skin isn't that white. When you narrow your eyes in suspicion or incredulity, for instance, darker shapes (the eyelids) overtake whiter shapes (the sclerae). Conversely, when you express surprise, the darker eyelids recede and open up more of the white sclerae. We look at muscular contractions in the brow area as well when detecting suspicion or surprise, of course, but color contrast between the eyelids and sclerae is also informative. The more varied and subtle an organism's emotional range becomes (i.e., more so in humans than other primates), the more crucial this information may become.

2) The study mentions that gaze-detection would be useful during mother-child learning, and John adds tool-making and tool use, but many cooperative behaviors would not be aided by gaze-detection -- namely, those where individuals are physically separated beyond the threshold at which judging another person's gaze based on eye movement becomes unreliable. I couldn't find any study quantifying this threshold, but I think at the range of about 40-50 feet, a moving head with stationary eyes would convey a stronger signal than a stationary head with moving eyes. If you recall any battle scene you've ever seen where two units were separated by such a distance, they usually communicate by jerking their heads or motioning with their hands and/or weapons, and surely combat is a cooperative and learning situation par excellence. Thus, it's really the close-range, intimate cooperative behaviors that are most facilitated by gaze-detection.

3) The news release mentions that "our eyes are more horizontally elongated and disproportionately large for our body size compared to most apes." That makes sense: if you're trying to detect a figure moving across a background, or the frame closing in or opening up by say 25%, these tasks would be easier if the background were larger on an absolute level.

4) It follows from the above three points that larger, whiter eyes would be of greater use to females than males. I tried Google and PubMed for info on sexual dimorphism of eye size and came up with this, though I can't access it. Hormones affect the eye, so there may be dimorphism. Judging from experience, it seems females do have larger eyes, though the magnitude isn't as pronounced as for, say, breast size or height. Dimorphism is slow to evolve, but we're talking about something that likely happened at least before the major human races diverged and sometime after we split from chimpanzees. The primate-human comparison apparently measures the area occupied by the eyes compared to that occupied by the face or body, but that may not be the best way to measure large eyes when the purpose of those large eyes is to make it easy to track the iris' movement. What you'd measure, then, would be the area of the visible iris divided by the area of the entire visible part of the eye. I think it's by this measure that you can tell girls have larger eyes, and that "babyfaces" like Johnny Depp and Pete Doherty do as well.

5) Once eyes become whiter and larger, they could be used to gauge a mate's health since discolorations due to infection will be more apparent against a white background, which would set off a round of sexual selection for more ornamental eyes. Thus does evolution strive to create Penelope Cruz, a dual-mooned beauty if ever there was one.

Borat's Cousin Horat   posted by TangoMan @ 11/19/2006 12:04:00 AM

We're reading a lot lately about how the producers of Borat set up ordinary citizens in order to mock them in the film and here we see how Sacha Baron-Cohen likes having the tables turned on him as his "cousin" Horat crashes the L.A. premiere and ambush interviews him. Sacha Baron-Cohen enters the clip at the 5 minute 30 second mark and I'd swear that the reaction we see is Baron-Cohen breaking from character.

Saturday, November 18, 2006

History repeating itself   posted by Razib @ 11/18/2006 04:08:00 PM

I'm reading God's War: A New History of the Crusades, and this on page 293 surprised me:
...Neither genocide nor forced baptism was canonically legal. However, some argued that these regions had accepted Christianity from missionaries in the previous decades and so could be regarded as apostates, thus action against them was, as in the Holy Land, a matter of reclaiming lost Christianity territory, theoretically defensive....

The regions in question were the pagan Slavic principalities between the kingdom of Poland and the German states. I was aware of the "Crusade" against the Wends, but I did not know of this specific justification. The backstory is that on occasion Wendish nobles would accept baptism and their immediate family would convert, but there was never any conversion of the general populace, so the claims that they were "apostates" are clearly ludicrous. I found the passage amusing because the logic maps perfectly onto to some of the specious arguments made by Islamists that all formerly Muslim lands (e.g., Spain, India, etc.) are still by definition Muslim and any attacks are "defensive." Justification by faith I suppose?

Will someone please think of the children?   posted by p-ter @ 11/18/2006 09:44:00 AM

Via AL Daily, I came across this somewhat bizarre essay on sociobiology in the Chronicle of Higher Education. It's by a professor of psychology, and the premise, ostenibly, is how evolutionary psychology should be taught in our schools to keep it from corrupting our youth. His solution:
Preferable, I submit, is to structure the teaching of sociobiology along the lines of sex education: Teach what we know, but do so in age-appropriate stages. Just as we would not bombard kindergartners with the details of condom use, we probably ought not instruct preteens in the finer points of sociobiology, especially since many of those are hidden even to those expected to do the teaching.
I can only assume this is tongue-in-cheek, or perhaps our dear professor hasn't been to a middle school biology class in a while--if he had, he would have noticed that evolution itself is not taught (or not taught well) in our schools. Forget the "finer points of sociobiology"; I'd be happy with the general points of evolution! It's like arguing whether the proper role of a garnish in drink-mixing should be taught in home ec; it's so far out of left field it leaves one puzzled.

Plus, even though the professor seems to have read some sociobiology, he parrots some of the classic misconceptions--he talks about selfishness as if it were uniformly beneficial in an evolutionary sense:
If the fundamental nature of living things - human beings included - is to joust endlessly with each other, each seeking to get ahead, then we're all mired in selfishness - a dark vision indeed.
He corrects this logic later, but even in doing so shows some odd assumptions:
For one thing, a deeper grasp of the evolutionary biology of altruism reveals that even though selfishness may well underlie much of our behavior, it is often achieved, paradoxically, via acts of altruism, as when individuals behave in a manner that enhances the ultimate success of genetic relatives. Here, selfishness at the level of genes produces altruism at the level of bodies. Ditto for "reciprocity," which, as Robert Trivers elegantly demonstrated more than three decades ago, can produce seemingly altruistic exchanges and moral obligations even between nonrelatives. Yet genetic selfishness underlies it all.
Unlike Richard Dawkins, who always made it clear that talking about genes as "selfish" was only a shortcut to predicting biological phenomenon, the author here seems to think that genes actually are selfish, and that this somehow has moral implications!

Friday, November 17, 2006

Race & Brazil - the sequel   posted by Razib @ 11/17/2006 08:38:00 PM

3 years ago a study came out which suggested that the color classifications in Brazil don't match that well to the ancestry as ascertained by loci which exhibit disjoint frequencies between Africans and Europeans. Yanni points me follow up study which agrees with the previous findings. You can read the pre-print here. Since 2003 a lot of material has come out on traits like skin color. We now know that around ~1/3 of the quantitative difference in complexion between Africans and Europeans is due to one locus which manifests in disjoint allele frequencies. Overall the work seems to be moving toward confirming the inferred genetic architecture derived from pedigree analysis that skin color as a trait emerges from the combine action of 4-5 loci of large effect. How does this relate to this study? Below I referred to "Ecotype Persistence" to define the perpetuation of adaptive alleles and phenotypes even when most of the local genetic pool is replaced by immigrant alleles.

Consider a contrived scenario. You have an island population which is coadapted to a local highland parasite. Sea levels drop and recontact is made with the parent mainland population. During the period of isolation genetic drift and local evolution has resulted in a non-clinal variance in allele frequencies between the "island" and "mainland" population. Even though reunited by a narrow isthmus assume that cultural barriers prevent a great deal of intermarriage. Also, let us assume that the mainland population is very large relative to the island population. If you had a small amount of intermarriage per generation the island population could be genetically assimilated to the mainland population rather quickly. If at a locus, A, there was a 1% replacement of "native" alleles with "mainland" alleles, within 2,000 years 2/3 of the alleles in the island population would be derived from the mainland. Now, consider another locus, B, which is implicated in adaptation to the highland parasite. If you assume that an "island" allele confers greater than a 1% fitness benefit vis-a-vis the immigrant "mainland" alleles, then it can persist indefinitely. 2,000 years later locus B will have preserved the ancestral character of the population, but locus A will be similar to the state of the mainlanders. In fact, on the vast majority of the genome the island population will be assimilated to that of the mainland, but on specific adaptively beneficial alleles the ancestral character will be maintained in the totality.

The point is to illustrate the power of selection in confounding our assumptions about genetic admixture and long term evolutionary dynamics when we use a population level lens. One reason that the ornate fantasies of early 20th century historical physical anthropology were so popular is that they appealed to our bias in imagining the movements of peoples across time & space, with the admixture of originally pure Platonic races. The imaginings of Madison Grant and company were only moderately more rooted in fact than the migrations of Tolkein's elves.

Which gets me back to the paper above. First, caveats. The original paper was met with a lot of skepticism. Some of it is probably warranted as the flavor of Political Correctness is pretty transparent in the author's text and statements from what I can see. Nevertheless, the beauty of science is the judgement of reality. Review the results yourself. One Brazilian commenter noted that they used one population in one village, but the individual didn't bother to read the original paper where they used some control groups in other cities to double-check their finding. Though I believe that the results need to be viewed as only part of the picture (e.g., I suspect there are plenty of unadmixed Europeans in the far south of Brazil, and nearly pure Africans in places like Bahia), I think they do capture some of the reality of racial admixture in that nation. The basic results were that though self-identified and researcher identified blacks, browns (in the sense of being mixed race) and whites did differ genetically, the difference was far less than one might have assumed and did not match what one would have predicted if phenotype and ancestry tracked perfectly. What happened here? First, remember that a few genes of large effect induce the skin color difference. Though racial ascertainment is a gestalt perception based on many variables, those variables are finite, a very small subset of visible characters controlled by a small number of genes which do not necessarily have to be reflected in the rest of the genome. The recent prominence of black and white twins born from mixed-race parents illustrates the issue: the relatively small number of characters used to judge race can quickly be reshuffled and segregated in a mixed population. Consider a population of white Brazilians, assume that a number, x, of white looking mixed-race Brazilians "passed" every generation. Though the loci which control physical appearance were predominantly derived from their European ancestors, these individuals would still carry and introduce a larger number of African alleles which do not exhibit any visible outward effects. Over a number of generations a non-trivial proportion of non-European ancestry could easily introgress into a population which is overwhelmingly European on loci which shape the outward phenotype. Conversely, more African looking mixed-race individuals would bring into the black population European alleles. What you see here is the power of social selection in maintaining modal phenotypes via assortative mating!

In the year 2056   posted by the @ 11/17/2006 10:10:00 AM

New Scientist asks: What will be the biggest breakthrough of the next 50 years?

Geoffrey Miller answers:

Applied evolutionary psychology should revolutionise life in three ways by 2056. First, Darwinian critiques of runaway consumer capitalism should undermine the social and sexual appeal of conspicuous consumption. Absurdly wasteful display will become less popular once people comprehend its origins in sexual selection, and its pathetic unreliability as a signal of individual merit or virtue.

Second, studies of human happiness informed by evolution will reveal ever more clearly the importance of "social capital" - neighbourliness, close-knit communities, local family support, and integration between kids, adults and the elderly. This will, I hope, lead to revolutionary changes in urban planning, leading to a New Urbanist revival of mixed-use landscapes. Enlightened citizens will demand to live in village-type spaces rather than alienating suburbs of single-family isolation and unbearable commutes.

Third, evolutionary moral psychology will reveal the social conditions under which human moral virtues flourish. The US will follow the UK in realising that religion is not a prerequisite for ordinary human decency. Thus, science will kill religion - not by reason challenging faith, but by offering a more practical, universal and rewarding moral framework for human interaction. A naturalistic moral philosophy will replace the rotting fictions of theological ethics. In these three ways, applied evolutionary psychology will help Enlightenment humanism fulfil its long-stalled potential to make us all brighter, wiser, happier and kinder.

s/will/ought to/ for a more reasonable way to think about that.

Thursday, November 16, 2006

Wade wades in....   posted by Razib @ 11/16/2006 10:56:00 PM

Nick Wade finally throws together a piece on Neandertals.

Update by agnostic: John Hawks also has a new FAQ on the implications and non-implications of the two new studies Wade reviews.

Basics: synapses   posted by amnestic @ 11/16/2006 10:52:00 PM

Of course you can look up what a synapse is and find a jillion explanations of dendrites, axons, and neurotransmission, but maybe you just wanted to casually check out the neanderthal news rather than actively seeking synapse education. So while you're browsing the web-o-tubes, I will direct you to a page containing some nice movies and images. There is a short, narrated animation concerning synapses.

Very briefly, synapses are where neurons talk to each other. Usually one neuron does the talking and the other listens. The talker releases chemicals called neurotransmitters into the synapse. The neurotransmitters float across the synapse until they bump into the listening neuron. Rather than ears, the listener has neurotransmitter receptors. The neurotransmitter binding to the receptor causes changes in the listener AKA the post-synaptic neuron. So when I say, for instance, that some experimental manipulation caused a change in the number of glutamate receptors, I am referring to the number of ears the listener has in the synapse. Glutamate is one of many neurotransmitters, but we'll do that some other middle-of-the-night.

Neandertal DNA, take II   posted by p-ter @ 11/16/2006 09:28:00 PM

As promised, this week's Science has an article from Eddy Rubin's group reporting 65 kb of Neandertal DNA sequence. It's not the million bases reported in Nature, but it's nothing to sneeze at, either.

In terms of admixture, they find no evidence for it, though they can't rule out low levels:
[T]he maximum likelihood estimate for the Neanderthal contribution to modern genetic diversity is zero. However, the 95% CI for this estimate ranges from 0 to 20%, so a definitive answer to the admixture question will require additional Neanderthal sequence data
This group is taking a different approach to their sequencing-- since the method they use generates data more slowly, they're not looking to get an entire genome anytime soon. Instead, they're going to look at loci of particular interest for human evolution:
Based on these results, we attempted to recover specific Neanderthal sequences from library NE1. We focused on recovering sequences that we had previously identified by shotgun sequencing because of the low complexity of library NE1, and were able to recover 29 of 35 sequences we targeted (table S4). The authenticity of these sequences was confirmed by the presence of library vector sequences in the reads. Our success in recovering both previously unknown cave bear and known Neanderthal genomic sequences using direct genomic selection indicates that this is a feasible strategy for purifying specific cloned Neanderthal sequences out of a high background of Neanderthal and contaminating microbial DNA. This raises the possibility that, should multiple Neanderthal metagenomic libraries be constructed from independent samples, direct selection could be used to recover Neanderthal sequences from several individuals to obtain and confirm important human-specific and Neanderthal-specific substitutions.
So once again, not a whole lot in terms of actual biology (though perhaps the anthropologists will take issue with that statement), but the proof of principle is there-- expect some big papers on "sexy" genes like ASPM, microencephalin, and FOXP2 in the coming years.

Exhaling genes   posted by rosko @ 11/16/2006 03:59:00 PM

From Epigenetics News:

Researchers at the Wadsworth Center, the public health laboratory of the New York Sate Department of Health, have shown it is technically feasible to detect DNA methylation using a simple breath test. Dr. Weiguo Han and Dr. Simon D. Spivack have tested seven patients by having them breath into a handheld device for 10 minutes, which forms a condensed vapor, to which the methylation assay is applied. The methylated form of all six tumor suppressor genes could be detected using the simple breath test.
    The DNA is believed to be released when cells turn over, or are damaged, in the lungs and airways, he said. “Although it is not possible to say at this point the precise anatomic origin of the airway-derived DNA being tested, it may be that different patterns of gene methylation will themselves actually map the origin of this DNA to particular regions of the airway,” Spivack said.

The researchers hope that the test can be further developed into a non-invasive test for the early detection of lung cancer.

From genomics and evolution to medicine   posted by p-ter @ 11/16/2006 01:28:00 PM

The most recent issue of Current Opinion in Genetics and Development has the theme "Genomes and Evolution: From genomics and evolution to medicine". There are a number of reviews of interest to readers here; check them out.

Neandertals...the continuing saga   posted by Razib @ 11/16/2006 12:06:00 AM

Two posts on my other blog, I try to show with pictures my own idea of the "3 models" of human origins, Multi-regionalism, Out of Africa, and the new model which Greg & John haven't christened yet. In another post I try to offer up when I see as the essence of the difference between Multi-regionalism and the new model (which I provisionally label "Ecotype Persistence").

John got so many hits today that he had to go on back up servers, but keep watching that space! There must have been a lot of querying for Neandertals today, I started getting referrals from this six month old post over at MSNBC about the topic because they linked to me!

Long time readers of the blog will note that the characterization of the Ecotype Persistence model is simply a glorified version of Henry Harpending's "Racial Diversity" post from the early years of this blog. In Race: the Reality of Human Differences Vincent Sarich marvels at human variation, and offers that selection must be powerful indeed to reshape a species as young as our own into so many different morphs. But Ecotype Persistence offers a way for us to ratchet down the god-like powers of selection, Sarich assumed that the variation in our species was a function of mutation from 50 K BP to the present as well as the extant genetic variation of the ancient African population. For such diversity to pop up with little raw material to work with clearly one would assume that selection is working 24-7 like a Korean clerk. But the extant genetic variation that might be available for local positive selection driven by ecological pressures might be orders of magnitude greater than Sarich assumed because novel alleles did not have exist in the African genetic background or emerge de novo. Modern humans could have "picked them up" through isolated interbreeding events and quickly shape-shifted to somewhat resemble the archaic homonids whom they were demographically marginalizing!

Addendum: Why do we assume Neandertals were hairy?

Wednesday, November 15, 2006

MAC vs. PC   posted by Razib @ 11/15/2006 08:40:00 PM

The nature of understanding and interest   posted by rosko @ 11/15/2006 04:17:00 PM

I just had a short conversation with one of my professors about one of my most common topics of discussion, namely the role of human understanding in science and engineering. He made a comment like "the most interesting things in the universe are ones we cannot understand", which seemed like a quite unusual thing to say. For me, there is basically no (intellectual) interest in things that I cannot hope to understand. I think this is part of the reason I am not much interested in the social scene. I insert the word "intellectual" simply to exclude things that are "interesting" solely because the result benefits or harms me personally, or members of the opposite sex I am "interested in" in the sense of attraction.

For me there is an interest, as sort of "beauty", that is initially present in almost all complex physical systems, and which disappears when they go outside the grasp of understanding. Again, beauty is in quotes because there are things that look beautiful in a non-intellectual way. I was wondering about whether people on here find that interest and understandability also go hand in hand. By "understandable" I don't mean simple, I just mean something that can be mentally captured in some way other than a series of equations impenetrable to anything but a computer.

A Neandertal genome in two years?   posted by p-ter @ 11/15/2006 04:06:00 PM

This week's Nature has an article from Svante Paabo's group analysing the first megabase (1 million base pairs) of sequence from the Neandertal genome. Coming out later this week in Science will be an article from a competing/collaborating group which is looking to accomplish the same goals using a different technique. So the Neandertal Genome Project(s) is well on its way:
In view of that prospect, we have recently initiated a project that aims at achieving an initial draft version of the Neanderthal genome within two years.
But a million base pairs is still quite a bit (though the human genome is around 3.3 billion bases); is there anything of major biological interest in this paper?

I'd argue no, this is essentially a proof of priniciple-- they've shown that ancient DNA can be sequenced in a large-scale, feasible way. But there are some tantalizing hints of what's to come:
[T]his high level of derived alleles in the Neanderthal is incompatible with the simple population split model estimated in the previous section, given split times inferred from the fossil record. This may suggest gene flow between modern humans and Neanderthals. Given that the Neanderthal X chromosome shows a higher level of divergence than the autosomes (R.E.G., unpublished observation), gene flow may have occurred predominantly from modern human males into Neanderthals. More extensive sequencing of the Neanderthal genome is necessary to address this possibility.

Tuesday, November 14, 2006

Genomics and socialized health care   posted by p-ter @ 11/14/2006 07:38:00 PM

On this site, we often refer to public genomics resources like the HapMap project when making an argument about population differences in one thing or another. The reason for this is simple-- there is a vast quantity of information freely available that allows, in the words of H. Allen Orr, "any bright graduate student working in his parents' garage [to] ask and answer any awkward question he likes." Come to think of it, that's not a bad description of this site, though bright graduate students thankfully make enough money to live on their own these days.

It's worth keeping in mind, though, that these excellent resources have not been assembled for the pedantic pleasure we get from skewering uninformed opinions about race. Millions of dollars have been spent in the hope that these resources will lay the framework for large-scale medical genetic studies--essentially studies that make robust correlations between particular genetic variants and disease outcomes. These studies are only now starting to appear, and the inital results are promising-- new variants have been found for obesity, diabetes, and heart disease. One goal of these studies is to discover new disease pathways which may be future therapeutic targets, but another is possibly more worrying-- the creation of a "risk engine" which will predict, for a given genome (i.e. your genome), the probability of developing any of a number of diseaes.

To be blunt-- our insurance system is in for a major overhaul. As a general approximation, we (Americans) are now charged for medical insurance based on how likely it is we're going to get sick and how costly that's expected to be for the insurance company. Non-smokers pay less. Obese people pay more. If your dad died of a heart attack, that's probably not something you want to mention when you apply for coverage. But with a full view of your genome, your expected eventual cost to an insurance company will be predicted even more precisely. There's no doubt that insurance companies will want this information, and under our current system, it's a perfectly legitimate request-- if you accept a priori that higher risk people should pay more for health insurance, you should certainly want to include genetic information in your risk calculations to increase the "efficiency" of the system.

Poltically speaking, this will be rather problematic. Essentially, there is a "genetic underclass" (to phrase this provocatively) more prone to disease, and you might well be part of it. Importantly, this categorization cuts across traditional boundaries of class-- while certain diseases might be associated with poverty, there will be people in all classes of life who are genetically prone to obesity, for example, and who will be forced to pay more for insurance. This will seem, to most people, "unfair". A couple possible political responses are as follows:

1. Make it illegal to use genetic information in determining health care coverage. This is possibly feasible, though I'm skeptical. Within a couple decades, your genotype might be on your chart from birth, and insurance companies will absolutely make use of it. Family history is already used; this would be a simple step further. And as I noted before, this is perfectly logical-- the more information available to them, the better their calculations, and the more efficient the insurance system.

2. I'm willing to advocate the alternative: strict, government-enforced indifference to genetic information-- that is, some version of socialized health care. Your genotypic information will be available, but all will be charged equally. The details need to be worked out, but other models are out there, including (dare I say it?) the French one-- a percentage of all costs covered by the government via a co-pay system, with supplementary insurance available on top of that.

The genomics revolution in biology will soon be showing some effects socially; a number of institutions will have to be questioned. Now seems like a good time to throw out some ideas of what comes next.

Frans de Waal   posted by p-ter @ 11/14/2006 05:34:00 PM

The most recent Current Biology has an interview with Frans de Waal. His take on public opinion of biology:
Apart from the perennial controversies surrounding evolution here in the USA - an issue beyond the grasp of my European brain - there have been dramatic changes in public opinion in favor of those who try to put human behavior in an evolutionary light. The days when Ed Wilson got doused with water are behind us. One can now say (as I like to do) that humans are essentially apes and suggest genetic influences on behavior without meeting the incredible hostility that marked the 1970s.

One time, long ago, I was attacked for claiming that male chimpanzees are dominant over females - how did I know this? wasn't I projecting male prejudices onto their society? - whereas recently, I attended a lecture where a speaker listed biologically based gender differences, a lot of them, and I saw young people in the audience yawn! Apparently, the effect of the Y chromosome on behavior has become a boring topic.

I lecture in many countries, and often end up in public debates. Until recently, I found the French most averse to Darwinian explanations. But even there, all of a sudden the sun has come through the clouds: comparisons between apes and humans are accepted when only a few years ago they were seen as deeply offensive. Evolutionary explanations are becoming all the rage among French intellectuals.

In about three decades, the general public in the West has moved from fear of biology to fascination. Now let's see if the social sciences will follow by putting more evolution into their thinking and curriculum. It is bound to happen

Nature vs Nurture & Science Personified   posted by amnestic @ 11/14/2006 04:27:00 PM

T-Rex is killin' it lately! - "I am on the lookout for science, personified!." "NATURE VERSUS NURTURE; in comic form, baby"

Monday, November 13, 2006

Austin W. Bramwell on conservatism   posted by Razib @ 11/13/2006 10:06:00 PM

I really don't know what to make of Austin W. Bramwell's piece for The American Conservative. He concludes thus:
Whatever its past accomplishments, the conservative movement no longer kindles any 'ironic points of light.' It has produced fewer outstanding books even as it has taken over more of the intellectual and political landscape. This trend will only continue. Worse, no reckoning will be made: they hope in vain who expect conservatives to take responsibility for the actual consequences of their actions. Conservatives have no use for the ethic of responsibility; they seek only to 'see to it that the flame of pure intention is not quelched.' The movement remains a fine place to make a career, but for wisdom one must look elsewhere.

Bramwell is a talented young lawyer, and his assault reads like the precise brief of a prosecutor bent on convinction. And yet, to where do we turn if all the various strands of conservatism stand guilty before us? Here's hoping that Bramwell has a follow-up in the works. Over the past few years following Bramwell's essays I get the sense that he is actually engaging in a game of intellectual Go, fleshing out the broad outlines through a process of negation and encirclement, but perhaps I'm just hopeful....

Addendum: Bramwell is married to the former Sarah Maserati. She is the fellow Episcopalian that Derb alluded to in his piece about religion. Austin Bramwell is a traditional Episcopalian himself. How do I know this? When Bramwell burst onto the conservative scene I went looking for some information....

Gene expression, chimp vs. human   posted by Razib @ 11/13/2006 08:18:00 PM

Some people say human geneticists suck. On the other hand, check this out, Conservation and evolution of gene coexpression networks in human and chimpanzee brains:
Comparisons of gene expression between human and non-human primate brains have identified hundreds of differentially expressed genes, yet translating these lists into key functional distinctions between species has proved difficult. Here we provide a more integrated view of human brain evolution by examining the large-scale organization of gene coexpression networks in human and chimpanzee brains. We identify modules of coexpressed genes that correspond to discrete brain regions and quantify their conservation between the species. Module conservation in cerebral cortex is significantly weaker than module conservation in subcortical brain regions, revealing a striking gradient that parallels known evolutionary hierarchies....

Here's the press release for the public.

Update by Darth Quixote: Useful Wikipedia articles for understanding this paper include DNA microarray, hierarchical clustering, principal components, multidimensional scaling, and functional genomics.

Alzheimer's a balanced polymorphism?   posted by amnestic @ 11/13/2006 06:51:00 PM

Alzheimer's = Sickle Cell. Severe Childhood Diarrhea = Malaria. Here's an older paper describing the association. The new report with mice isn't out yet.

Arc-o-mania   posted by amnestic @ 11/13/2006 12:32:00 PM

The new Neuron has FIVE, count'em FIVE, articles on the protein, Arc. This protein gets made in all the right places and at all the right times to be important for synaptic plasticity and memory, but nobody knew what it did. Now we have clues that it might actually help pull AMPA-type glutamate receptors out of the membrane. One of the models presented suggests a role in setting the overall level of excitability allowed for a cell, so if some synapses are getting strengthed others have to take a hit. More later when I get a chance to really read. I recommend starting with the Tzingounis and Nicoll review.

Related; BDNF and Arc regulation: NMDARs vs AMPARs

Update: Upon finishing Chowdhury et al., I note that they found a ~2-fold increase in the amount of surface GluR1 (a subunit of the AMPA receptor) in neurons from the Arc knockout mouse, but in figure 4 of Plath et al. there is no change in basal synaptic transmission in these mouse. The only way I know to resolve this is for the surplus of AMPA receptors found by Chowdhury to be somewhere that they can't affect transmission (i.e. not in the synapse).

Erratum: Rial Verde et al, citing the Chowdhury paper states that Arc interacts with the SH3 domain of endophilin. This is not the case. The experiment they performed on the basis of this statement is still okay because they are really just concerned with blocking the interaction between Arc and endophilin, but the domain of endophilin that Arc interacts with is a helix within the BAR domain which has a curved structure thought to normally interact with the curved lipid membrane of endocytic vesicles. (sorry for the jargon). Here's some wikipedia for endocytosis. Check the clathrin-dependent kind, that's how receptors are pulled out of the membrane. Pulling receptors out of the membrane would decrease the impact of neurotransmitter release, weakening the synapse.

Molecule of the Month   posted by amnestic @ 11/13/2006 12:27:00 PM

Go learn something about blood-clotting and look at some pretty structures at the Protein Data Bank's Molecule of the Month archive.

Saturday, November 11, 2006

Species and introgression   posted by Razib @ 11/11/2006 02:46:00 PM

John Hawks has a long post on introgression in the context of the Species Concept problem.

Friday, November 10, 2006

"Diversity"   posted by Razib @ 11/10/2006 07:00:00 PM

I was talking to a friend of mine who is a postdoc @ M.I.T., and he said the following:

...if you want to see diversity, come to MIT. There's people from all over the world....

Of course, it's not the right kind of diversity. Diversity which emerges out of merit is deemed less worthy than the mystical communion with that ineffable concept of Diversity which contemporary Americans adhere to just as medieval Christians held to the Trinity: you never consider questioning it, but no one truly understands what it is.

Adam Gopnik on Darwin in The New Yorker   posted by Razib @ 11/10/2006 06:31:00 PM

Rewriting Nature, Adam Gopnik's essay in The New Yorker is now online.

(via Afarensis)

Memory enhancement by non-invasive electrical stimulation   posted by amnestic @ 11/10/2006 05:09:00 PM

Nature reported and Robert Stickgold commented on a study by Marshall et al. They trained folks to remember some wordpairs and then stuck electrodes on their scalp while they were sleeping. By providing rhythmic stimulation across the cortex they were able to increase the amount of time spent in a specific sleep stage: slow-wave sleep. You know some sleep stages, right? Like REM is the sleep stage where you're dreaming and things like that. Slow-wave sleep is a non-REM stage. The volunteers that received this stimulation remembered word pairs better than the ones who did not. Slow-wave sleep is especially interesting because a characteristic cortical rhythm called a "sleep spindle" can be recorded during that time, and other studies have shown that firing of hippocampal cells becomes coordinated with that of cortical cells during these patterns.

Our results indicate that slow oscillations have a causal role in consolidating hippocampus-dependent memories during sleep. How could slow oscillations promote the plastic neuronal changes that underlie such memory consolidation? One plausible mechanism might involve calcium transients mediated by spindle activity2, 23, 24, as spindle activity was enhanced by slow oscillation stimulation. Not only is spindle activity probably associated with massive Ca2+ influx into neocortical pyramidal cells, but there is also evidence that repeated spindle-associated spike discharges can trigger long-term potentiation in neocortical synapses25. As synchronous spindle activity occurs preferentially at synapses previously potentiated by tetanizing afferent stimulation26, slow-oscillation-driven spindle activity might contribute to the strengthening of synaptic connections in neocortical circuitry.

They ran lots of control memory tasks and found that the enhancement was specific for declarative memory (the wordpair test) as opposed to motor learning tasks. I might've like to see an attentional or working memory task on the second day to show that the sham-stimulated group weren't just groggy or something.

Thursday, November 09, 2006

What do you do with Creationists?   posted by Razib @ 11/09/2006 07:42:00 PM

Dean Esmay graciously linked to our recent discussion of Neandertal introgression, and there was this comment:
I'm of the opinion that "Neanderthal," as we know it, is the scientific equivalent of smoke and mirrors designed for the expressed purpose of supporting evolution. They've allowed the cart to pull the horse. Evolution must be right therefore there must be evolutionary stages. Since the former cannot ever be questioned anything coming from it is simply fruit from the poisonous tree.

Unsurprisingly I take a Biblical approach. We see in the Bible that man lived for hundreds of years....

Now, my own initial response was that this was a satirical comment, but subsequent comments and clarifications from regulars on Dean's blog confirmed that this individual was a Creationist. Their argument is rational, assuming Creationist priors. Seeing as how a really cool evolutionary story just broke I really wasn't going to waste my time arguing Creation vs. Evolution. When Creationists post on the weblogs I run or manage I simply delete their comments, I see no point in even insulting them or caling them out. There just isn't a plausible way to bridge the discussion, and I'm interesting in understanding evolution, not debating whether gravity exists or not.

My question is for readers, and it is two fold:

1) What do you do or say when confronted with Creationists? When I was younger I would debate and engage my peers who were Creationists (many of my friends), and at this point I've felt like I put in my dues. When someone expresses Creationist sentiments now I simply write them off and perform a silent intellectual shiv'ah.

2) Nevertheless, I do feel it is important that some individuals do speak up on this topic. I applaud Ken Miller for taking the battle to the Creationists, someone has to do it. What's the optimal strategy so that real science can continue without interruption?

TangoMan adds: This New Scientist article addresses the rise of a whole separate creationist educational system - here's a scary quote:

Home-school parents are able to teach their children this way thanks mainly to a group called the Home School Legal Defense Association (HSLDA), a non-profit organisation based in Purcellville - like Patrick Henry College (PHC), which the HSLDA founded. . . . .

Now evangelical home-schoolers can also opt for a college like PHC. The school was founded in 2000 to "prepare leaders who will fight for the principles of liberty and our home-school freedoms through careers of public service and cultural influence".

It worked. By 2004, PHC students held seven out of 100 internships in the White House, a number even more striking when one considers that only 240 students were enrolled in the entire college. Last year, two PHC graduates worked in the White House, six worked for members of Congress and eight for federal agencies, including two for the FBI. "Patrick Henry is something to worry about because these kids end up in the administration," says Glenn Branch, deputy director of the National Center for Science Education in Oakland, California, which campaigns against the teaching of creationism as science.

Home-schoolers are drawn to PHC partly because of its political connections and partly because, unlike most Christian colleges, it boasts high academic standards. Besides the focus on creationism, much of the curriculum is dedicated to rhetoric and debate, preparing students to fight political and legal battles on issues such as abortion, stem cell research and evolution. The technique is effective. For the past two years, the college has won the moot court national championship, in which students prepare legal briefs and deliver oral arguments to a hypothetical court, and has twice defeated the UK's University of Oxford in debating competitions.

Derek Lowe needs a job by year's end   posted by Razib @ 11/09/2006 12:43:00 PM

Derek Lowe needs a new job soon. I know that some recruiters read this weblog. Here is his "about":
Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.

Living Neandertals - visual "evidence" (?)   posted by Razib @ 11/09/2006 10:56:00 AM

Wednesday, November 08, 2006

All Neandertal all the time.....   posted by Razib @ 11/08/2006 11:06:00 PM

I'm posting a crap load of Neandertal related junk over at my other weblog (more scheduled). I wonder if John is going to keep it up. As I note on my other blog two popular articles on the Paabo group's work just came out, which makes me suspicious re: timing. I would keep track of google news, query Neandertal and MCPH1. Even Slashdot got in on the action. I'd also track technorati for Neandertal and MCPH1. And for what it's worth, I'm guessing that the "living Neandertals" are on the Celtic Fringe.

The male oral contraceptive...   posted by p-ter @ 11/08/2006 02:06:00 PM
Share/Bookmark on its way.

The pill apparently targets germ cells while leaving testosterone and other hormones untouched. If side effects are negligible, this could be big. Clinical trials await...

Four Stone Hearth II   posted by Razib @ 11/08/2006 07:54:00 AM

Four Stone Hearth over @ Afarensis' place today.

Neanderthal introgression & microcephalin   posted by gcochran @ 11/08/2006 05:53:00 AM

A few years ago, I was thinking about Out-of-Africa, and it occurred to me that we probably picked up a lot of favorable alleles from Neanderthals, the logic being that such alleles would have probability 2s per copy (Haldane) of reaching high frequency (maybe even going to fixation). The chances of acquisition of a neutral allele (from a single introduced copy) was 1/2Ne; so, for s = 5% and an effective population of 10,000, that allele with the 5% advantage was 2000 times more likely to make the interspecies jump. Therefore mtDNA stats really told you nothing.

So as we spread out into Neanderthal territory, even a few tens of interspecies matings would have let us scarf up most of their good genes. Individuals from every pair of mammalian sister species with comparably recent common ancestry are interfertile, so it was a good bet that this actually happened. This seems to happen frequently in invasive weed species, by the way. They arrive, they hang around the docks for a few years, stealing the good alleles from related local species - then they go forth and conquer.

Looking at the new article in PNAS, I'd say that Bruce Lahn and company have probably found one. Read it.

Now if the Neanderthals were really effectively isolated before we expanded into their territory, they'd have a lot of significantly different alleles. Some would have involved various kinds of regional adaptations, which might be a good thing to have in Eurasia. (MC1R?) But it's entirely possible that some alleles solved adaptive problems that had existed in Africa as well - but solved them better.

Brains had expanded over the last half-million years in both Africans and Neanderthals, but it seems likely that those changes in size and structure were driven by different mutations, just as light skin in Europe and East Asia was. The Neanderthals had slightly bigger brains than Africans: obviously those brains were useful for _something_. Anyhow, in this kind of convergent evolution of sister species, there can be lots of alleles worth stealing. When we select for the same trait in multiple lines, sometimes we get higher values of that trait by hybridizing a couple of the best-performing lines. Also, since the Neanderthals were ecologically different (cold weather, high risk hunters & pure carnivores), they might have been able to evolve some adaptations that just couldn't happen in Africa (different constraints, different topography of the fitness surface).

Maybe Africans and Neanderthals 'nicked'. Any farm boy, looking at the timeline of African expansion, encounter with Neanderthals, and the subsequent 'great leap forward', should have suspected hybrid vigor. It's corny but it makes sense.

So when you think about the cultural explosion that occurred shortly after we overwhelmed the Neanderthals (cave paintings, sculptures, new tools and weapons, all that jazz) - well, you have to wonder if assimilating a passel of adaptive alleles in a few thousand years, way more than the typical number that would arise and become established over such a short time span, didn't give us a hell of a boost. There are signs of behavioral modernity a bit earlier in Africa - but those ostrich eggshells are dull as hell compared to Gravettian cave paintings. Expansion out of Africa must itself be a sign of new capabilities (I'd bet on sophisticated language) but you only see full-fledged behavioral modernity in the European Upper Paleolithic... Judging from neutral genes, it can't have happened often, but those few furtive human-Neanderthal couplings may well played a crucial role in the future development of the human race. I'm sure that this notion will suggest new pick-up lines to some readers.

If this pans out the way we think it will, introgression from Neanderthals (and maybe with other archaics) may have been one of the two fundamental patterns underlying recent human evolution.

Update by Darth Quixote: John Hawks has more here and here.

Tuesday, November 07, 2006

Did Modern Humans Get a Brain Gene from Neandertals?   posted by Razib @ 11/07/2006 05:37:00 PM

Read about it here. Here is the paper, Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage:
At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy {approx}37,000 years ago and swept to exceptionally high frequency ({approx}70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans {approx}1.1 million years ago and introgressed into humans by {approx}37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.

The full paper is free. Read it, bitches. More to come soon.... (commentary, plus papers)

Update by Darth Quixote: The D haplogroup is the same version of MCPH1 that has nearly fixed in many human populations outside of sub-Saharan Africa, as reported at Gene Expression last year (Bruce Lahn's brain on ASPM and MCPH1). Here is the Cliffs Notes part of the new paper's Discussion:

In this study, we investigate the origin of the microcephalin D allele in modern humans. We show that the D allele is unlikely to have arisen within a panmictic population. Instead, our data are consistent with a model of population subdivision followed by introgression to account for the origin of the D allele. By this model ... the lineage leading to modern humans was split from another Homo lineage, and the two lineages remained in reproductive isolation for ~1,100,000 years. During this period of reproductive isolation, the modern human lineage was fixed for the non-D allele at the microcephalin locus, whereas the other Homo lineage was fixed for the D allele. These two alleles are differentiated by a large number of sequence differences accumulated during the prolonged isolation of the two populations. At or sometime before ~37,000 years ago, a (possibly rare) interbreeding event occurred between the two lineages, bringing a copy of the D allele into anatomically modern humans. Whereas the original D-bearing Homo population has since gone extinct, this introgressed copy of the D allele in humans has subsequently spread to exceptionally high frequency throughout much of the world because of positive selection.

Update by Jason Malloy: Post up @ MetaFilter.

Monday, November 06, 2006

David Rowe's final paper   posted by the @ 11/06/2006 08:46:00 PM

The January 2005 issue of American Psychologist was devoted to the subject of race. As Steve pointed out at the time, most of the issue was complete fluff, with the exception of the paper by David C. Rowe. Rowe had died 2 years earlier, and wrote the paper during the convalescence prior to his death.

The article makes several points, which might have been better presented as a series of article. We can forgive Rowe for not taking the time. The final point is an outline of a research project that could "convincingly demonstrate a genetic origin of racial [IQ] differences." Rowe first suggests the use of multilocus DNA tests to estimate individual ancestry among African Americans. The measures of individual ancestry would then by compared with IQ scores and other measures to control for social/cultural confounding (Rowe suggests skin color). Moving beyond bulk comparisons of individual ancestry, Rowe suggests that MALD (mapping by admixture linkage disequilibrium) be used to associate ancestry at individual regions of the genome to IQ. MALD is the technique that Rowe suggests would "convincingly demonstrate a genetic origin of racial differences." I agree that this would work, but I don't know if any research finding could "convince" people.

R.C. Cooper thinks this is a terrible idea. In fact, Cooper seems to say that everything about Rowe's suggestion is a bad idea, including the utility of MALD. This appears to be a version of the Cavalli-Sforza squid ink effect. Cooper has subsequently published studies using MALD to examine hypertension among African Americans. If executed, Rowe's proposal would taint Cooper's research platform with charges of racism. His kitchen-sink refutation of Rowe's proposal makes sense in this light.

Headbanging hematoma   posted by amnestic @ 11/06/2006 08:41:00 PM

PubMed is weird. I was searching for information on 'stereotypy' as a statistical technique. 'Head banging' during rock show causing subdural hematoma. If anyone knows anything about the former could you toss me a link?

Another funny title on my search. Stereotypy of Predatory Boring Behavior of Pleistocene Naticid Gastropods. That article sounds really NOT! exciting! (watch a Borat trailer)

Most people are idiots, and other good news for democracy   posted by p-ter @ 11/06/2006 02:38:00 PM

On the eve of the midterm elections, a piece on the irrationality of voters. Excerpt:
But why are there some areas-- like politics and religion-- where irrationality seems especially pronounced? My answer is that irrationality, like ignorance, is sensitive to price, and false beliefs about politics and religion are cheap. If you underestimate the costs of excessive drinking, you can ruin your life. In contrast, if you underestimate the benefits of immigration, or the evidence in favor of the theory of evolution, what happens to you? In all probability, the same thing that would have happened to you if you knew the whole truth.

In a sense, then, there is a method to the average voter's madness. Even when his views are completely wrong, he gets the psychological benefit of emotionally appealing political beliefs at a bargain price. No wonder he buys in bulk.

(Via Hit and Run)

Place and Plasticity: Two Views on the Hippocampus   posted by Coffee Mug @ 11/06/2006 05:00:00 AM

"There are places I remember / all my life / though some have changed."

Step right up to see the tiny horse. The tiny seahorse. The brain structure mildly resembling a seahorse. The relatively large brain structure mildly resembling a ram's horn. Every time we think we get the hippocampus nailed down it squirms out of grasp. Anatomically and functionally it can be lumped in with a larger structural formation referred to as the hippocampal formation, or it can be divided into hippocampal subregions based around curving cell layers: the CA (cornu ammonis) fields, 1 and 3 being the clearest and best understood, and the dentate gyrus. There is too much to know about the hippocampus. It is studied for its pattern completing and separating computational properties, its rhythmic electrical field potential oscillations, its deceptively simple trisynaptic wiring diagram, its role in modulation of the stress response, the birth of new neurons in the adult dentate gyrus, the plasticity of its synapses, the response of its cells to spatial information, and its role in autobiographical memory of events. I will focus on the last two: spatial representation and episodic memory. Both aspects are areas of ongoing research generating controversy and debate within the field, and they have significant overlap. It may become apparent as we dig deeper that they are two sides of the same coin and that investigating each provides insight into the other.

Temporal Lobes and Temporal Gradients

The contemporary era of hippocampus research really kicked off in the 60s and 70s. There were hints that the hippocampus might be related to memory before then, but a breakthrough came in 1957, when patient HM, suffering from intractable epilepsy for 11 years, had large portions of his medial temporal lobe on both sides removed to eliminate the epileptic foci. If you picture the brain as a boxing glove, the temporal lobe is where the thumb would be. The medial temporal lobe is the part of the temporal lobe nearer to the middle of the brain, where the thumb touches the rest of your brainfist. The hippocampus runs along the inner side of this lobe from thumbtip to thenar and, depending on the species might curve up to the first joint of the index finger. When HM had his medial temporal lobe removed his epilepsy was cured, but his memory was severely disrupted. Specifically, he could remember new experiences for a short time so long as he wasn't distracted, and he could remember experiences form his remote past. He was not capable of storing new long-term memories or recalling recent memories.

Two major aspects of the hippocampus' relation to memory arose from studies with HM and other patients like him. One was the idea of memory taxonomy that separates memories that can be recalled as 'mental time travel' returning to the spatiotemporal context where the experience happened. This type of memory is referred to as episodic memory and contrasts with procedural memory, for instance, in which motor or coordination tasks are learnt. HM would probably be able to learn to ski, but he would not remember the process of learning. Memory taxonomy is not yet clear. A lot of terminology has been invented, but because recollection is a subjective experience it is hard to assay accurately in humans and especially hard to test for in animals. The second idea arising from HM's deficits was that of a temporally graded retrograde amnesia. The memories acquired more recently, in the years just prior to surgery were much more greatly affected than those from HM's childhood. This led to the idea that recently acquired memories spend some time stored in the hippocampus as a waystation before they take off to permanent storage sites in the synapses between various cortical neurons.

The literature nowadays is conflicted and disconnected regarding the idea of a temporal gradient. It has taken a while to discover memory tasks that test the sort of memories we expect the hippocampus to handle. A favorite is contextual fear conditioning, but it is still frustratingly complex. A rat is supposed to learn about a context by combining all the information about its surroundings coming from different sensory processing areas into an index such that re-exposure to just a partial set of the initial context cues can reactivate the memory of the whole experience. To be concrete, if the context smells like acetic acid, the light is red, and there is a fan blowing in the background, the rat might just need the smell to bring all the rest of the context flooding back. In contextual fear conditioning, a rat learns to associated a context with shock, presumably via hippocampus to amygdala connections. A temporal gradient for contextual fear conditioning was reported in 1992 by Kim and Fanselow, now a classic, highly cited paper. They trained rats in this task and then lesioned the dorsal hippocampus at various times afterwards (retrograde lesions). The rats that received lesions a day after training forgot to be scared in the context, whereas rats that received lesions a month after retained their memory. This is a perfect analog for the story of HM in rat years. Recently acquired memories are more vulnerable to hippocampus lesions.

The theory that the hippocampus is only a temporary memory storage site is called "systems consolidation". Remember how the hippocampus is supposed to pull together information from different sensory processing areas? In systems consolidation theory, the memory is rehearsed with those same areas until they get wired together and can reactivate the memory independent of the hippocampus. There are many reasons to like systems consolidation theory, but there are complexities. Here is one example. Kim and Fanselow didn't lesion the whole hippocampus. An alternative story to systems consolidation is the multiple trace theory. Rather than moving the memory out of the hippocampus, the memory representation could become distributed in the hippocampus up and down the dorsal-ventral axis making it more impervious to small lesions. Nadel and Moscovitch have been major proponents of the multiple trace theory and recently reviewed the human memory literature, even questioning the original interpretation of HM's deficits. One issue is how to ascertain whether a memory is truly episodic or is merely semantic (memory for facts that doesn't require autobiographical recollection; think rote memorization). For instance, I can tell you from my semantic memory what Neil Armstrong said after his first steps on the moon, but when he tells you the same thing he is re-living an episode from his life in a way that requires a type of processing that the hippocampus is especially good at. Using tests more sensitive to this distinction, HM has recently been reevaluated and found to have amnesia for episodic memory across his entire life.

This is a potentially devastating blow for systems consolidation theory, but the discussion continues. New papers have reported temporal gradients for retrograde amnesia in other hippocampus dependent tasks in animal models. Studies using activation markers and multi-electrode recordings are providing new evidence of post-training hippocampal-cortical communications and coordination especially during sleep. Part of the reason the new multi-unit recording studies are so provocative is that they allow a strong link between our understanding of the hippocampus as a memory storage device and another major theory of the hippocampus: cognitive map theory.

Grid cells and Gridlock

Perhaps the best way to understand the cognitive map theory of the hippocampus is to look at a place field. This is a two-dimensional map of an environment that some rat is exploring. The line tracks the path taken by the rat during the rat and marks red where firing of a particular cell rises above some threshold. Note that there is a bright red hotspot in the upper right hand corner. You would call this the place field for the cell being recorded in this experiment.

O'Keefe and Dostrovsky provided the first observation of place cells in 1971. When they recorded electrical signals from the hippocampus of a rat as it explored an environment they found that some cells had a fairly low basal firing rate, but would fire much more rapidly while the rat was in a specific part of the environment. There is a cell in your hippocampus that fires when you are standing at the foot of your bed and another for when you are in your shower. Actually, the cells remap if the environment is distinguishable as an entirely new context, so you might have two separate maps for the bedroom and the bathroom. O'Keefe and Nadel built on the idea that the hippocampus is responsible for encoding spatial information to create the theory of the hippocampus as a cognitive map. They proposed that our perceptions help produce and are represented in relation to a spatial framework in the hippocampus which we use to figure out where we are and where we're going. In humans, the cognitive map is the framework for storing memory for events in a spatiotemporal context. You could imagine, for instance, that your location is the anchor for your memory of events. What's the most important thing to establish at the beginning of a work of fiction? The setting.

The cognitive map theory is not without its critics and controversies, but I don't want to get bogged down in it. These are exciting times for place cell researchers. A great deal of enthusiasm has surrounded the discovery by the Moser lab in Trondheim, Norway of grid cells. Grid cells are very similar to place cells, but they serve a different purpose. They are found in the entorhinal cortex which is the last stop for sensory information being funneled down to the hippocampus. Rather than firing in one specific place field, grid cells have a triangular-grid shaped receptive field. Once again, it is easier to show than say.

Grid cells solve the problem of navigation in a novel environment. Place cells are consistent within a familiar enviroment, but it takes a little while for them to form their preferences upon exposure to a new room. How does one keep track of position when you don't have a map yet? Zork fans know the answer. If you went two spaces north and two spaces east, you can go two spaces southwest and get back to the room where the elf stole your jeweled key or whatever. It's called path integration. You sum the vectors of your movements to add up to the total displacement from your starting point. To turn this into a map of the white house with a boarded front door, you might start with a fresh piece of graph paper. The regularly repeating structure of spatial representation in grid cells serves the same purpose. They provide a framework for you to build a map inside.

A memory is more than just where you were though. It also includes a sequential order of events. Simultaneous recording of large numbers of place cells in the hippocampus has allowed the investigation of the sequential/temporal aspect of memory by way of patterns of spatial experience. I will provide one example from earlier this year. Foster and Wilson recorded from many place cells as a rat moved down a linear track like you or I would walk down a hallway. They move at relatively constant rate in one direction and eat some food at the end. The place cells that represented location during the previous trek down the hallway can fire action potentials while the rat is chillin' out at the end, eating his reward, and they do it in a rapid meaningful sequence. The cell closest to the end of the hallway kicks it off and the one at the beginning of the hallway is at the end. These and other sequentially organized patterns in the hippocampus might bring the firing in close enough proximity to be characterized as coinicidental. Coincidental firing is the first sign to the nervous system that maybe these two neurons ought to be hooked up to each other, so later when the memory of one portion of the hallway is recalled you are able to traverse across synaptic bridges to the rest of the house. There are also hints that this sort of sequential replay may occur during sleep and coincide with activation of neocortical areas, providing links between sleep, memory, and systems consolidation theory.

Another popular example of the special relationship between space and the hippocampus is the story of the London cabbies. London cabbies have to memorize the spatial layout of the city to an incredible level of detail. Imaging studies have revealed the hippocampus of a London cabbie is shaped differently than your average person; some parts are bigger and some are smaller. Greater volume differences are associated with more years of experience as a taxi driver. The obvious implication is that learning and using all those map details really works out their space muscles, growing more cells or larger cells in the hippocampus, and reorganizing according to the demand. This isn't entirely implausible since the hippocampus is one of only two confirmed sources of newborn neurons in the adult brain. There are alternatives though: the simple act of driving in the city with the attendant stress, motor planning, and cognitive demands might affect the hippocampus. A recent update attempted to control for these issues by comparing cabbies who have to really know the maps to bus drivers who do the same amount of driving without the memorization requirements. The volume differences hold up, and what's more, taxi drivers had more trouble learning new spatial information. This finding hints that there may actually be a limit to storage capacity for spatial information, which is not something we run up against day-to-day. Of course, the caveat that correlation is not causation remains. People with funny-shaped hippocampi might just have a predisposition to become cabbies and stick with it, but the study authors point to some evidence suggesting that initial spatial capabilities don't correlate with hippocampus shape suggesting that this alternative isn't strongly supported.

Memory for places or places for memory?

The discovery of place cells clearly indicated that the hippocampus represents where we are, but the discovery of grid cells in the entorhinal cortex reallocates a good-sized portion of that responsibility. Why then are the cells that should be handling memory wasting their time representing spatial location at all? One possibility is that location is the framework in which we embed our memories. A recent issue of the journal, Hippocampus, contained a collection of articles suggesting a strong correspondence if not isomorphism between the characteristics of place cells and memory. Sheri Mizumori provided an excellent introductory article profiling areas of overlap and distinguishing features of these two processes. For instance, certain drugs affect memory and place field representation in the same direction, and place fields become more refined as rats gain more experience in an environment. As a more concrete example, a study in 2003 reported changes in the response properties of place cells after fear conditioning. After establishing the place field representation in exploring, the study's authors delivered a tone paired with an aversive stimulus. Afterwards, place cells became responsive to tone and location. The cells of the hippocampus are capable of responding to more than just place, but place still held a primary role. A cell could only fire in response to the tone if the rat was in its particular preferred location.

Exploration of the hippocampus' abilities continues. I have not scratched the surface even in this mega-post. The theories of the hippocampus as a memory storage device and a cognitive map are not mutually exclusive and may turn out to be one and the same. I came to an interest in the hippocampus via a more philosophical route: considering the role of memory in the definition of the self and such, but there are plenty of noble non-navel-gazing reasons to delve deep into this structure as well. The hippocampus shows signs of damage and deterioration early on in Alzheimer's disease and other forms of dementia, and the same recurrent excitatory connectivity so useful for memory storage may also provide the substrate for the electrical storms underlying epilepsy. I hope you now have some more of the conceptual framework necessary for reading and evaluating new hippocampus articles, and we can talk about it some more when good studies come out. Now make like a hippocampectomized rat and get lost!

Cylons Discovered in Japan   posted by TangoMan @ 11/06/2006 12:30:00 AM

The Cylon home world has been discovered - it's Earth, and the Cylon nexus is Japan.

The Japanese drive to avoid the societal turmoil that often accompanies immigration has made them world leaders in robotic technology as they seek to develop robots to do the work of low-skill immigrants.

Their latest models are startlingly human-like.

Yahoo has a photo spread here, BBC has a story here, the Discovery Channel has a report here, and here's a YouTube video.

Sunday, November 05, 2006

Hirsutism and genetic diversity   posted by agnostic @ 11/05/2006 11:00:00 PM

On Comedy Central I just saw Russell Peters (admixed South Asian and British, superficially more of the former), and figured I'd watch since stand-up comic routines are a great source of data for HBD issues that are taboo elsewhere (Comic View on BET is always reliable). In the clip below, skip and watch the bit from 2:45 to 6:00 if you haven't already guessed where this is going.

Now, we've covered hairiness in humans before (here and here), but the focus was mostly on the difference between homo sapiens and other primates. But as Peters clearly lays out -- and as always comes up whenever we discuss which ethnic group's females are hotter than which other's -- this trait varies substantially enough between populations that it's obvious to anyone who isn't blind and who's had even a little experience with the relevant groups. But the reasons for this variation seem even less clear than those behind the chimp-human variation. Continue below the fold for data on hirsutism and some (hopefully) educated speculation on why it varies between groups. Leave your own (hopefully) educated speculation in the comments.

Beginning with definitions, hirsutism in women is measured by some version of the Ferriman-Gallwey score, which tests different areas of the body for varying degrees of hairiness from 0-4 in increasing hairiness (example combinations). It seems the consensus is that scoring 3 is sufficient to qualify as hirsute for women -- for example, light hair on the upper lip, lower back, and chest would get an FG score of 1*3 = 3. This trait is not normally distributed: most women score low (2 or less on a scale of 0-36, where 36 = 4 points max per 9 areas measured), so you'd have to model it with a log-normal, gamma, exponential, or other such distribution. If you wanted to apply La Griffe's method of thresholds, then, you'd have to change the quantile score from the skewed distribution -- say it's log-normal -- to the z-score of the normal distribution, according to:

Q = exp(m + qs)

Where Q is some quantile score for the log-normal and q the corresponding z-score from the normal distribution, with m and s the normal's mean and SD. Using the standard normal with m = 0 and s = 1, the above simplifies to:

Q = exp(q)

It might be simpler still to just apply the method of thresholds to the log-transformed Q values instead of the Q values themselves (to reduce effects of skew) in order to estimate the difference in means between groups. Not being a math wiz (relatively speaking), I simply note the choices to be made, present the data below, and leave it to those more skilled at modeling to resolve.

Now, to the rough topography of the hairiness map. What data I've found through PubMed suggests that the stereotypes about body hair are true, so in the absence of data on a particular population, going with your gut is probably safe assuming you've had minimal experience with said group. First, a recent study found no difference in hirsutism between Whites and Blacks in the southeastern US -- given the region, most likely the Whites are northern European and the Blacks sub-Saharan African, from the West most likely (cite):

MAIN OUTCOME MEASURES: Terminal body hair growth was assessed using the mFG scoring system; nine body areas were scored from 0-4 for terminal hair growth distribution. RESULTS: The mFG scores were not normally distributed; although cluster analysis failed to identify a natural cutoff value or clustering of the population, principal component and univariate analyses denoted two nearly distinct clusters that occurred above and below an mFG value of 2, with the bulk of the scores below. Overall, an mFG score of at least 3 was observed in 22.1% of all subjects (i.e. the upper quartile); of these subjects, 69.3% complained of being hirsute, compared with 15.8% of women with an mFG score below this value, and similar to the proportion of women with an mFG score of at least 8 who considered themselves to be hirsute (70.0%). Overall, there were no significant differences between Black and White women.

That fits with most people's experience that Blacks don't appear any more or less hairy than northern Europeans. But who's even less hairy? East Asians, of course! Even in patients who have elevated levels of hormones which tend to lead to greater body hair, the Japanese women were not hirsute, while the American and Italian women were (cite):

RESULTS: Women from Japan were less obese (p <>, although the percentage of cystic ovaries (68% to 80%) was comparable. Serum luteinizing hormone, testosterone, and estradiol were similar, but levels of 3 alpha-androstanediol glucuronide, which was elevated in women from the United States and Italy, was normal in women from Japan. The adrenal androgens, dehydroepiandrosterone sulfate and 11 beta-hydroxyandrostenedione were elevated in 48% to 64% of the patients and by a similar percentage in the three groups.

The same appears true for Southeast Asians such as Thai women (cite):

RESULTS: Five hundred and thirty-one women underwent a physical exam. The women who had the total hair-growth score of 0, 1 and 2 by mF-G-L method accounted for 97.8% of all the subjects. All of the 11 subjects with a total score of 3 or more considered themselves to have excessive growth of hair.

So, only 2.2% of representative Thai women were hirsute compared to the 22.1% of northern Europeans and sub-Saharan Africans mentioned above -- an order of magnitude less! Who's more hairy than northern Europeans and s-S Africans? The Greeks, of course! Take the following with a grain of salt, since it was taken from a representative sample of a Greek island (Lesbos), and it's well known that island people may turn out weird due to founder effects, inbreeding, and what-have-you. But Lesbos is very close to other Greek islands and to the heavily populated part of Turkey that borders the Aegean Sea and the Sea of Marmara. Bearing that in mind (cite):

To determine the prevalence of PCOS [Polycystic Ovary Syndrome -- agnostic] in the Greek population as well as the metabolic parameters, we performed a cross-sectional study of 192 women of reproductive age (17-45 yr), living on the Greek island of Lesbos. They were divided into 4 groups according to the presence of hirsutism (defined as a Ferriman-Gallwey score > or = 6) and O/M: group N (n = 108), regular menses and absence of hirsutism; group 1 (n = 56), regular menses and hirsutism; group 2 (n = 10), O/M and absence of hirsutism; and group 3 (n = 18), O/M and hirsutism.

Then (56+18)/192 = 38.5% of the sampled women were hirsute. This is actually an underestimate since in this study the threshold was not an FG score of 3 or greater but a more stringent 6 or greater! Again given the skew of the hirsutism distribution, a more realistic estimate might be somewhere around 50% scoring 3 or greater. As for Spaniards (cite):

Hirsutism was defined by a modified Ferriman-Gallwey score of 8 or more . . . PCOS was present in 10 (6.5%), hirsutism was present in 11 (7.1%), and acne was present in 19 (12.3%) of the 154 women.

Without a clear understanding of the exact shape of the distribution, we can't know what percent of Spanish women scored at just 3 or greater on the FG scale in order to compare them with the above studies, since the Spaniards were judged hirsute only if they measured 8 or greater. It seems reasonable to assume that on average the Spanish are equally or somewhat less hairy than the Greeks, but hairier than northern Europeans, s-S Africans, and NE and SE Asians. The only data I could find on New Worlders was a not representative sample of Mexican-American women who'd been pre-selected for a family history of coronary artery disease. Thus the following is certainly an overestimate, especially since the hirsutism data were self-reported rather than measured on the FG scale (cite):

Using the questionnaire to diagnose PCOS, we found that 20 (13%) of the 156 women studied met criteria for PCOS (self-reported irregular menses and clinical signs of hyperandrogenism). In the remaining women, 17 (11%) reported menstrual abnormality only, 71 (46%) reported hyperandrogenism only, and 41 (31%) reported no abnormalities.

Then, for what it's worth, 0.13 + 0.87*0.46 = 53.0% of this selected sample were hirsute. As we've mentioned before, Mexican-Americans are not Amerindians -- they are admixed, so it could well be that even correcting for the bias in the above sample, much of the rest may simply reflect admixture from hairy Mediterranean populations. At least from what I've seen from National Geographic or The Discovery Channel, the indigenous of the Americas are more like East Asians in hairiness.

And to bring it back to Russell Peters' original remark, the only study that looked at hirsutism among South Asians and Caucasians (most likely Britons) did so as part of a larger study on PCOS (cite). Among the 47 South Asian and 40 Caucasian women who had PCOS, the median FG score was 18 for the former and 7.5 for the latter (P less than 0.0001); and even among the 11 South Asian and 22 Caucasian controls, the median FG score was 8 for the former and 1.5 for the latter (P less than 0.04). So, South Asians are clearly much hairier than northern Europeans, regardless of having PCOS or not. It should be noted, though, that 40 of 47 South Asians with PCOS and 9 of 11 South Asian controls were Pakistani, and consequently 29 of 47 of those with PCOS and 4 of 11 of the controls came from consanguinous backgrounds (which is more prevalent in Pakistan). None of the Caucasians with PCOS or controls were from consanguinous backgrounds.

To summarize the picture so far, it looks like hairiness is most frequent in the area from roughly Greece through the Middle East and into South Asia, is perhaps somewhat lower in the rest of Mediterranean Europe, is lower still in northern Europe and s-S Africa, and lowest of all in NE and SE Asia (and likely among the Amerindians as well). This inter-group variation clearly reflects "recent" evolution, as in after the major continental races went their separate ways; and given the northern European - Mediterranean difference, this may reflect even more recent evolution, as in the past 10,000 years. Neutral drift is out of the question. Though hairiness may not be at fixation in South Asia, by all accounts it's close enough for government work. Since the time in generations for the fixation of a single mutation = 4Ne, where Ne is the effective population size, let's make the generous assumptions that this neutral drift began 10,000 years ago rather than more recently, and that 1 generation = 20 years rather than some longer estimate like 25 years. Then, under these assumptions, the effective population size from which this emerged would only have been 125! That's not the same as census size, for sure, but it's still off by at least an order of magnitude. As usual, neutral drift is unlikely to be informative about evolution in large, non-founder populations over a "recent" timescale for functional traits (and vice versa).

We rehashed a lot of adaptationist accounts of why humans are hairless for primates in the threads linked to at the beginning of the post -- adaptation to climate, protection against ectoparasites, etc. But the split between relatively more and less hairy populations doesn't mirror the two big splits of the past 10,000 years, both a result of the agricultural transition: 1) increasingly complex societies, which likely selected for higher IQ; and 2) a shift in diet and pathogen stress. Hairiness clearly doesn't track social complexity or current mean IQ of different groups, and it's not clear how hairiness would help or harm integration into more or less complex societies. Neither does hairiness appear to track dietary changes, though there may be some subtler difference in one particular foodstuff I'm unaware of that does carve up the world the same way hairiness does. And if it reflected recent changes in pathogen stress, you'd expect it to slice up the world into one group containing s-S Africans, Middle Easterners and South Asians, and Southeast Asians; and another containing northern Europeans, Amerindians, and NE Asians. This mapping seems the least erroneous of those examined -- perhaps pathogen stress might account for some substantial fraction of the variance, even if not a majority of it. However, this still seems unsatisfying since most recent changes in pathogen stress involve really nasty fuckers like malaria, small pox, measles, plague, and so on -- so we'd expect a response that kicked into gear earlier than puberty.

Which brings us to the next area of explanations: sexual selection. The fact that women of various parts of the world vary significantly between racial and ethnic groups, but are apparently close to the levels of their co-ethnic males, would fit the pattern of slow dimorphism. Since body hair sets in at puberty and declines somewhat with old age, it seems likely that this is a secondary sex characteristic even among females. Clearly no male would prefer this trait, so it's conceivable that females were sexually selecting males who had masculinely hairy bodies, and that their children -- sons and daughters alike -- inherited alleles that predisposed to hairy bodies. Presumably, over a long stretch of time this might become more dimorphic, so that South Asian females would come to resemble Swedish females in body hair, but as Russell Peters notes, we've arrived at a cultural point where hair-removal is relatively cheap and commonplace. Thus, the alleles may persist at their high frequencies among the hairier populations since their effects (at least as regards male choice) will be largely mitigated by cultural innovation.

We already know that females from more pathogen-stressed environments emphasize "good looks" in a male mate more than do females from less-stressed environments (Gangestad & Buss 1993). And this study suggests that at least some degree of body hair is attractive on males. So it could be that, for whatever other reason, South Asians and nearby populations were slightly hairier than s-S Africans (who also select for good looks due to pathogen stress), but that this difference was magnified by sexual selection in the former areas but not the latter, if we assume there was less variability in hairiness in older s-S African populations relative to older South Asian populations. Perhaps due to small differences in local ecology, hairlessness is under tighter functional constraint in s-S Africa and SE Asia, while it's not in other germ hotspots like South Asia and the Middle East. Evolution is stochastic, after all. Well, I took a shot at it anyway. What better ideas are there that are consistent with the data outlined here?

Amongst the halfings   posted by Razib @ 11/05/2006 07:23:00 PM

From Twilight People, a chronicle of a black American with a Coloured mother as he journeys through that community in South Africa:
...As we made our way to our table, we crossed paths with some of the most striking and exotic-looking people I'd ever seen: olive-skinned women with blonde hair and blue eyes; men with reddish brown skin and mos pf dark, curly hair; girls with alabaster skin, aquiline noses, full lips, and gray-blue eyes; boys with the swarthy complexion of Italians and straight, sandy brown hair....

The dominant Christian Afrikaans speaking element of the Coloureds are an admixture between Dutch European males, as well as slaves from Asia, and African slaves of Bantu, and especially, Khoikhoi origin.

Neandertal introgression   posted by Razib @ 11/05/2006 10:23:00 AM

Hawks on Neandertal introgression:
The bottom line is that the bones are modern (i.e., not Neandertal), but they include features that are common in Neandertals. Almost all the other European bones of early Upper Paleolithic date also have Neandertal features. The number and frequency of such features in this earliest Upper Paleolithic sample are greater than in any later sample.

In other words, they look like they have genes from Neandertals. And those genes declined in frequency or effect over time.

Diversity Training in Action   posted by DavidB @ 11/05/2006 01:20:00 AM

From today's UK Sunday Times, an amusing account of a training course in 'diversity'. It is a straw in the wind - I doubt that this would have been published, at least in a major newspaper, only a few years ago. I particularly liked the following:

"What do you expect from today's course?" asks Harvey [the trainer] brightly. "Why did you come here?" "Because we've been told we have to," says one woman with brutal honesty. A male colleague is even more frank. He is bald and stocky, and looks - by his own description - like a thug. "I've been on lots of these before," he says, tucking a pencil behind his ear, "and I'm interested to see which racial group is fashionably more equal these days."

Saturday, November 04, 2006

Brother-sister differences in the g factor   posted by Darth Quixote @ 11/04/2006 10:48:00 PM

In press at Intelligence, from the redoubtable Ian Deary and his colleagues:

There is scientific and popular dispute about whether there are sex differences in cognitive abilities and whether they are relevant to the proportions of men and women who attain high-level achievements, such as Nobel Prizes. A recent meta-analysis (Lynn, R., and Irwing, P. (2004). Sex differences on the progressive matrices: a meta-analysis. Intelligence, 32, 481-498.), which suggested that males have higher mean scores on the general factor in intelligence (g), proved especially contentious. Here we use a novel design, comparing 1292 pairs of opposite-sex siblings who participated in the US National Longitudinal Survey of Youth 1979 (NLSY1979). The mental test applied was the Armed Services Vocational Aptitude Battery (ASVAB), from which the briefer Armed Forces Qualification Test (AFQT) scores can also be derived. Males have only a marginal advantage in mean levels of g (less than 7% of a standard deviation) from the ASVAB and AFQT, but substantially greater variance. Among the top 2% AFQT scores, there were almost twice as many males as females. These differences could provide a partial basis for sex differences in intellectual eminence.

Related: Women and science, sex differences, Lawrence Summers.

Ahmad Chalabi   posted by Razib @ 11/04/2006 09:13:00 PM

The New York Times Magazine has a story about Ahmad Chalabi. I think we should invade Iran just to get the files which could prove once and for all if that guy is an Iranian mole!

Savage   posted by Razib @ 11/04/2006 08:54:00 PM

Saudi court sentences rape victim to 90 lashes

A Saudi court has sentenced a gang rape victim to 90 lashes of the whip because she was alone in a car with a man to whom she was not married.

The sentence was passed at the end of a trial in which the al- Qateef high criminal court convicted four Saudis convicted of the rape, sentencing them to prison terms and a total of 2,230 lashes.

The four, all married, were sentenced respectively to five years and 1,000 lashes, four years and 800 lashes, four years and 350 lashes, and one year and 80 lashes.

A fifth, married, man who was stated to have filmed the rape on his mobile phone still faces investigation. Two others alleged to have taken part in the rape evaded capture.

O believers, did god not make you with hearts and does he not see all that you do??? Jesus Christ! Frankly, this kind of shit is why I get tired of the interminable without-god-all-is-permissible style of arguments, I mean, how big is the sample space of unexplored perversion and barbarity out there that all seeing god is deterring?

Update: Since we're on the topic, A New Generation of Adults Bends Moral and Sexual Rules to Their Liking:
To what extent does faith make a difference among Busters? The research shows that born again Busters - a group defined not based upon self-identification with the 'born again' label but based upon their beliefs about Jesus Christ and regarding life after death - were different from non-born again young adults on some issues. Born again Busters were somewhat less likely to illegally download music, to smoke, to view pornography, to purchase a lottery ticket, or to use profanity. However, young believers were actually more likely than non - believers to try to get back at someone and to have stolen something. Moreover, on eight of the 16 behaviors, the profile of born again Busters was virtually identical to that of non-born again Busters.

So, no more bullshit about how religion can encourage morality without a citation of studies. I'm tired of reading your introspection.

Accelerated human evolution in non-coding regions? (reprise)   posted by p-ter @ 11/04/2006 03:37:00 PM

The other day, I mentioned a paper in Science claiming that non-coding regions have played a large role in human evolution. In the paper, the authors devise a new test for finding human-lineage-specific evolution, and apply to to a number of conserved non-coding regions in the genome. The new method seems pretty useful--it takes into account both locus-specific neutral evolution rates and lineage-specific constraint. As I mentioned before, they find 992 regions in the genome with human-specific acceleration. But how many would they expect to find by chance? An important question, and one they answer in the Supplementary Materials online:
By the definition of P-values, the expected number of CNSs in any P-value bin of width w is w*110,549 under the null model of constrained human lineage evolution (w = 0.00125 in Figure 1). Thus, we expect only 553 human-accelerated CNSs at a P-value threshold of 0.005 (0.5%), though we observe 992 (0.9%). The false-positive rate in the set of predicted accelerated CNSs is therefore ~56% (553/992).
Hey now! That's a pretty serious false positive rate. So to revise my previous thoughts, they definitely show some non-coding sequences have undergone a human-lineage-specific acceleration. Other groups are getting similar results, so I'm not going to doubt that. But that false positive rate seriously calls into question their conclusion that the accelerated regions are preferentially found hear genes involved in neuronal adhesion--it's tough to argue about the characteristics of a set of regions if more than half of them don't belong in the set at all.

Further, and this is a question that has been bothering me about a lot of papers on human evolution, where do you go from here? Now they have a set of 992 candidate regions that could play an important role in human evolution, but more than half of them are false positives--how do you decide which ones to follow up? It's almost enough to make a guy consider doing "real", wet biology...

The Russo-Iranian Eurasian axis   posted by Razib @ 11/04/2006 02:53:00 PM

From the ever sage Matt Yglesias:
Susan alerts me to this music video for "Vostochnaya Skazka" an international super hit from Russian girl group Blestyashie in which they collaborate with Iranian pop sensation Arash. The resulting song is bad. Very bad. Troublingly bad. It's especially disturbing that Arash appears to live in Sweden, which has traditionally been the Anglosphere's main ally in the quest to make the world safe for non-awful popular music. If they defect to the Eurasian Crap Pop Bloc, all may be lost.

Some of the lyrics are funny:
At one point in the lyrics, Arash says, says "Hey beautiful girl, I really like you. I already have three wives but you can be the fourth." Then the girls are all, "Look dear, I already have 5 husbands. I love them all, but if you want, you can be the sixth."

Friday, November 03, 2006

Announcing the blog of the Uberclass   posted by Razib @ 11/03/2006 11:27:00 PM

In case you don't know it, The Economist has a blog. The nation-state is dead! Long live the nation-state!

The MIT hiring issue   posted by amnestic @ 11/03/2006 10:19:00 PM

I really enjoy Susumu Tonegawa's work and writing. He runs the Picower Institute for Learning and Memory and has produced some of the most technically sophisticated transgenic manipulations to answer memory questions. It's too bad he got himself in a little hot water earlier this year. Apparently, there are major competition issues between the different institutes and departments involved in neuroscience research at MIT, and they heated up to an unhealthy level this past spring. ScienceNOW has the whole story and the ad-hoc committee's report. The report deals out the blame pretty evenhandedly across departments and department heads. I like how the McGovern Institute head basically answers to nobody.
The fracas began when a young neuroscientist named Alla Karpova declined a position at MIT's McGovern Institute for Brain Research. As her reason, she cited resistance to her appointment by Nobel laureate Susumu Tonegawa, who heads the rival Picower Institute for Learning and Memory at MIT. Karpova's supporters say Tonegawa sent e-mails to Karpova that were inappropriate and intimidating and that senior MIT officials refused to intervene. When the matter became public in July (Science, 21 July, p. 284), MIT Provost Rafael Reif set up a panel to investigate the situation across campus, including at the two institutes.
As for Karpova, the report says MIT's effort to recruit her was "unusual and flawed in many ways." Karpova, now a postdoc at Cold Spring Harbor Laboratory in New York, is moving in June to the new Janelia Farm research campus of Howard Hughes Medical Institution outside Washington, D.C., where she will become a group leader.
In the end, Janelia Farm is a damn fine place to end up. It just looks way cooler than MIT and appears to have a similar ridiculous level of resources and star-studded faculty roster.
In response to the report, MIT will establish a neuroscience advisory panel, led by materials scientist Lorna Gibson, to tackle the broader issues troubling the program. But MIT biologist Nancy Hopkins, who has led an ongoing effort to put the issue of women faculty on the university's agenda, criticized "this indecisive response by the administration." Hopkins says that the university's response to date "perpetuates destructive behavior by senior faculty and administrators against young scientists, particularly women," while damaging neuroscience at the university.
Where've I seen that name before? Oh... Here she is.. ''I would've either blacked out or thrown up."

Borat   posted by Razib @ 11/03/2006 08:31:00 PM

Saw Borat today. Funny, but too much fecal/toilet humor for my taste. I paid matinee price so I'm happy, would be a little let down if I'd gone full price. Also, from wiki:
Parts of the film were filmed in Romania, not Kazakhstan, and some characters purporting to speak Kazakh are really speaking Romanian. Also, Sacha Baron Cohen speaks Hebrew in the film (not Kazakh), while Ken Davitian, the actor who plays Azamat, speaks Armenian. They also use several sayings from Slavic languages, such as Polish or Czech.

That makes sense, the language seemed all over the place.

Derb has some semi-spoilers...and I pretty much agree with him on the issues he brings up.

Kuffar vs Muslim rappers   posted by agnostic @ 11/03/2006 01:39:00 PM

Religion is like sports -- you either care about it or you don't, and I don't. However, over at Razib's ScienceBlogs page, there are some potshots taken at White kuffar rappers, with a video of "Informer" by Snow as the evidence against allowing Whitey to rap. [1] How ironic, as a duo of pop musicians from Muslim countries has covered this very song -- in Farsi and Urdu! Lyrics. Unlike Snow's, they're intelligible, and the refrain "dil bole boom boom yeh" means "my heart says boom boom yeah" -- easy enough to understand. The guy is Arash, a Persian who moved to Sweden at age 10; and the girl is Aneela, a superfine butt-kickin' Dane of 1/4 Persian, 1/4 Pakistani, and 1/2 Indian background. (Also recall that a recent Miss Denmark was half-Brown.) If only all goofy rap songs could be re-worked into vehicles for Perso-Indic salaciousness (check out the part around 2:10).

[1] As an aside, as much crap as White rappers take, no one ever mentions how much worse it would be if Northeast Asians were rappers. This is one of those things you're not supposed to mention since only Whitey is allowed to be slammed for lack of rhythm and rhyming skills compared to Africans. But of course, Europeans have a higher average Verbal IQ compared to NE Asians, who excel at Spatial IQ. Though the consequences of this cognitive profile difference as it affects differing musical skills across groups are not crystal clear, it's still obvious that rapping is custom-tailored to individuals who are better at verbal than spatial tasks and who are extraverted braggarts. We'll have to wait and see how Eminem's reputation fairs throughout the decades, but by far the most eminent White rappers (going on 20 years in their craft) are a group of Ashkenazi Jews from Brooklyn: The Beastie Boys. As for Brown rappers, their sub-population also seems to excel at Verbal more than Spatial IQ, and South Asian music falls into the more verbal-ish style (focus on melody, rhythm, and improvisation, rather than elaborate harmonies). But as Razib reports, the results are mixed.

Thursday, November 02, 2006

Accelerated human evolution in non-coding regions?   posted by p-ter @ 11/02/2006 07:06:00 PM

We've discussed the roles of protein-coding sequence change to non-coding change in human evolution before. A new article in Science claims to add more support for the role of non-coding changes. In a set of over 100,000 conserved non-coding regions in the genome, they identify about a thousand with significant acceleration along the human lineage. Interestingly, these regions are enriched near genes involved in neuronal cell adhesion, suggesting...well, something vague about the evolution of cognitive traits.

The methodology used in the paper is supposedly laid out in the Supplementary Information online, but I don't see it there. But hopefully, this will be an interesting new method for detecting accelerated evolution in non-coding regions. I'll probably comment more once I get a hold of the methods section and can make more intelligent critiques.

Yes, Virgina, there is a God. And he lives off the coast of New Jersey.   posted by p-ter @ 11/02/2006 06:53:00 PM

You know how little kids write letters to Santa, laying out their claims on His glorious, chimney-borne bounty? Isn't that just so god-damned cute? We pat them on their heads, smile and nod, and wink at the others in on the joke. But what happens when those kids grow up and write letters to God? Cute? Comical? Or just horribly depressing?

RNA activation   posted by amnestic @ 11/02/2006 02:57:00 PM

I can't find the original research article yet, but Science has a news article about a finding from the UCSF lab of Rajvir Dahiya indicating that small RNAs can activate genes instead of inhibiting them. The discovery of RNA interference recently led to a Nobel. Small double-stranded RNAs can be chopped in two by the cell and carried around as templates to find other RNAs with matching sequences. When these target RNAs are found they are usually destroyed or at least sequestered. Instead, these folks are reporting on observation of the opposite effect. The targeted gene is activated to produce more protein. CRAZY!! This is really nice in terms of gene therapy. I kept dreaming up schemes to activate genes that we need more of by inhibiting their inhibitor, but this is so much simpler... maybe...

A note of caution, the double-negative inhibition thing could still be what's happening here:

One key question is whether Li's RNAs are activating genes by silencing others, which would just be RNAi by another name. For example, proteins called negative transcription factors can prevent genes from being transcribed; silencing the genes for these proteins could activate genes they control. Although the UCSF group has not found evidence that this is happening, "formally, that's still a possibility," says Rossi.

Islam and Science @ Nature   posted by amnestic @ 11/02/2006 02:34:00 PM

Nature is offering a free collection of articles on Islam and Science.

Kamal El Helbawi, who now lives in London, is a one-time senior official in the Muslim Brotherhood, and its former spokesman in Europe. In common with, arguably, most Muslims, Helbawi sees science and Islam as being in harmony, and he says that any government led by the Muslim Brotherhood will reverse decades of underinvestment in R&D. Is this a rose-tinted view or a genuine commitment? The answer may depend on the resonance of science and technology with the wider debates occurring in Muslim society. It may also depend on whether Islamist parties lean towards the Shia or Sunni schools of thinking (see 'A long tradition', page 24).

For Helbawi, science has three functions in society. First, it is a set of tools to help humankind enjoy a higher quality of life through new technologies or by solving problems that afflict the poor. Second, science and technology can be used to deter aggression, a justification, Helbawi believes, for developing a nuclear deterrent. And third, Helbawi believes that science has a role in strengthening religious belief. In his view, the Koran, in addition to being the word of God, was designed by God to convince doubters of the truth of Islam and of creation. "I urge all scientists to read the Koran, from which they will learn much about so many scientific topics," he says.

I'll get right on that.

Perhaps more compelling is the open letter from 114 Noble Laureates attempting to intercede in the matter of five nurses the Libyan government has all but decided to go ahead murder on accounta some kids caught AIDS while they were working in the hospital.

Wednesday, November 01, 2006

Veils, part n   posted by Razib @ 11/01/2006 10:28:00 PM

Talk of the Nation had a segment on the full face veil today. A few points:

1) One of the guests, who wore a full face veil, basically implied that women who don't dress the way she does are sluts. OK, not really but it was close enough. Her basic contention was that dressing the way she does sends a signal to men that she wants to be respected, that she has good morals, and is not an object. But the reality is that we need to frame this in its proper context. Yes, compared to Dirty Aguilera the contrast is stark, but there is a wide range of dress between black-moving-object and barely legal. The recent firestorm over the Australian cleric who compared women who went unveiled to "pieces of meat" who invited rape is simply another elaboration on the same general thrust, so to speak. There are particular cultural sensibilities common among many (not all, see below) Muslims that seem bizarre in the West. Getting drunk at a frat house and not bringing back up is really bad news for a woman, walking down the street in pants and a t-shirt is generally not a situation of clear and present danger.

2) The problem here is that social context matters. Today, a one piece swim suit is relatively modest beach attire in the West. Not so 100 years ago. In much of Europe toplessness is accepted as normal on beaches, but here in the United States it is very transgressive. Social norms differ. Now, it is true that men are extremely lascivious visual creatures, but, the "I'm a slut" signal differs from culture to culture, because sluttiness is a matter of scale and relativity. To be perceived as modest and not draw attention in the West doesn't necessitate taking up the niqab, or, frankly even the hijab. If one has an absolute scale of modesty this might not be so, but, if the concern is how others perceive you, then that is the reality. Similarly, dressing a certain way that might seem modest in the West in Muslim countries might necessarily invite unwanted attention (e.g., short-sleeved shirts). Social context matters, you aren't an island.

3) Which brings me to the point about attention. One of the callers was a Muslim convert who declared that a) she believed that the niqab was necessary for her practice of Islam b) resented the insults and intimidation that she received from others around her due to her wearing a niqab. I addressed what I feel are the basic human necessities which make the veil (as opposed to the hijab) problematic before, so I will simply focus on the social context again: by wearing the veil a woman makes herself covered meat who invites abuse. Now, I am being unfair and consciously echoing what the cleric above said. There is no excuse for abusing and intimidating women in public because of how they dress, or don't dress, but there is a social reality that exists. In public places I have regularly seen "goth" or "punk" kids being abused, taunted or mocked. When I lived in Pennsylvania some of the rougher kids would make sport by mocking the Amish, and even running off with their hats and making fun of their clothing when they had to come into town (to put in perspective how pathetic these creatures were, recall that the Amish are pacifists and so they would never fight back). Wearing the veil is a statement, just like getting a lot of peircings, or tatoos, or dying your hair is a statement. If the goal is to be modest and keep a low profile, walking around in a full body veil is not doing that. That's just the reality.

4) If you listen to the interview you'll note that not all the Muslims are particularly comfortable with the veil. This is an important point which needs to be reiterated: wearing a fully veil is an interpretation of Islam. By analogy, interpreting the Bible "literally" is a particular way of viewing Christianity, but it is not necessary for Christianity. I'll be honest that I'm not particularly excited by the gymnastics and accommodations that the US government makes for religious practices, that being said, that's the reality. If the government perceives that practice x is necessary for major religion y, then steps to accommodate will be taken. Once those steps are taken a feedback loop may emerge which defines the cultural trajectory that that religion takes in shaping and defining itself.

5) Finally, a major problem that I think needs to be addressed is that veiling was never really normal in any society that is like a typical Western society where women are independent and are out and about in the world. The report notes, as usual, that veiling was an elite practice common in the ancient world which was adopted by Muslim ruling castes. There were women who had a bevy of servants and lived secluded lives in their own compounds, complexes and places. There are only two types of societies which I know practice ubiquitous veiling

a) Primitive and underdeveloped tribal societies like Afghanistan
b) The oil rich Gulf states

The only reason that "modernity" (in regards to amenities) exists in Saudi Arabia concurrently with massive sex segregation and veiling is that oil wealth subsidizes this lifestyle. In places like Afghanistan women and men live very separate social lives, and society is segmented into tightly knit clans. I have known of Muslim women who have veiled themselves fully in the West who never made waves, because they never left their own house. Yes, some Gulf Arabs who come to study in the USA and bring their family simply cloister their women as they do in the mother countries. The problem is when women want to venture out into the big wide world as normal peers with men and non-Muslim women, but they want to dress like they live in a cloister! In the end to satisfy women who want both to dress and interact as if they live in the court of King Khosrau and have a fullfilled life in a technological society we might have to transform Earth into Solaria.

Addendum: Let me also state that of course Muslims are correct that men are fixated upon the physical form of women and sex. But, I do not believe that Muslim societies themselves have particularly healthy attitudes toward this topic, and, there are many general "unnatural" aspects of liberal democratic societies as a whole. The separation that full veiling entails seems to come with costs which I believe are problematic for a republic of citizens equal before the law and naked before their peers.

Charlie Rose on the brain   posted by the @ 11/01/2006 07:12:00 PM


Interesting bits:
1. Rose asks about geographical/population differences in brain structure/function -- maybe Jim Watson and E. O. Wilson rubbed off on him -- but there were no takers. A follow up on sex differences gets a few answers, including the suggestion that lack of male plasticity after stroke could be a result of firmer specialization that would produce "faster" processing in some domains.
2. The NIH scientist appears to mention the Turkheimer study on the heritability of IQ varying with SES but get the results backwards.

The art of seduction   posted by p-ter @ 11/01/2006 06:17:00 PM

Speaking of Machiavelli, here's an amusing passage from the New Yorker's profile (not online) of Robert Greene:
Greene is not a libertine. Drawing upon a list of the nine seducer types in his book (the Coquette, the Charmer, the Dandy, the Natural, etc.), he is, as he told me, "a reformed Rake." (Reformed rakes live in a constant danger or recidivism.) He lives with his girlfriend, Anna Biller, a filmaker and old-Hollywood fetishist, on whom he practiced some of the tactics suggested in "The Art of Seduction." Having seen her around Santa Monica, he got himself invited to a party at her house, where he slipped away to study her record collection. Afterward, he invited her to a Dubussy opera that he knew would appeal to her. Still, the victim resisted. So he asked her to his thirty-seventh birthday party. He also invited seven other attractive women, friends who, at his bidding, did little to dispel the impression that they might be sleeping with him. It worked. He and Biller have been together for ten years.
A move straight out of gc's playbook?

Resveratrol   posted by the @ 11/01/2006 04:29:00 PM

David Sinclair's group has published (in a rush) their work on the health and longevity benefits of Resveratrol in mice. Nicholas Wade has good coverage in the NYTimes and Nature has a podcast, a news article, and the research article.

In Wade's article, Sinclair says he, his family, and his lab are taking it at a lower dose than that reported in the Nature article. Have any of you been taking it? Wikipedia, for what it's worth, suggests there are problem with pharmacokinetics in pure resveratrol preparations.

I assume that resveratrol itself cannot be patented, but Sinclair's company is reportedly in the middle of clinical trails with a patentable (and more effective?) resveratrol analog.

MicroRNA binding sites under selection in humans   posted by amnestic @ 11/01/2006 09:24:00 AM

Using data from the HapMap project Chen and Rajewsky compared the density of single nucleotide polymorphisms (SNPs) in computationally predicted microRNA binding sites. SNPs are small changes in the nucleotide sequence that may or may not have big effects. If evolution likes a gene just the way it is then it will do its best to suppress polymorphism, so low SNP density is a hint toward negative selection. But low SNP density could also just mean a low mutation rate. Apparently, there is a technique referred to as derived allele frequency (DAF) analysis that gets around this by comparing the human polymorphisms with the ancestral sequence (chimp or macaque). I don't understand DAF analysis. Maybe someone else can explain it. Point is, this is evidence for negative selection on microRNA binding sites in humans.

They also found evidence for a SNP that was recently (within the last 50,000-70,000) positively selected in Africans. The SNP they identified is present in 87% of Africans and almost completely absent in Europeans and Asians. It is in the miRNA binding site for Map1lc3b, more popularly known as MAP1B (microtubule-associated protein 1B). MicroRNAs generally repress synthesis of whatever protein they bind. The authors don't mention whether this SNP is likely to increase or decrease the stability of binding between the miRNA and the MAP1B-RNA. They do mention that misregulation of this gene has been linked to disorders such as giant axonal neuropathy and fragile X syndrome. The protein disrupted in fragile X is itself a translational suppressor, so there could be some synergy here in the fragile X phenotype.

Microtubule associated proteins often stabilize the microtubules. These are long filaments made up of polymerized tubulin subunits. Microtubules are the cell's molecular highway. Little semis made of kinesin and dynein proteins traverse up and down the microtubule highway and carry cargo such as dendritically targeted RNAs to their destination. So one function of this SNP might be to subtly alter how many lanes the highway has at some overpasses. On the other hand, according to the abstract below, MAP1B affects neural development as well. Guess it is still way too early to say.

Microtubule-associated protein 1B function during normal development, regeneration, and pathological conditions in the nervous system. J Neurobiol. 2004 Jan;58(1):48-59.
Gonzalez-Billault C, Jimenez-Mateos EM, Caceres A, Diaz-Nido J, Wandosell F, Avila J.

Microtubule-associated protein 1B is the first MAP to be expressed during the development of the nervous system. Several different approaches have revealed that MAP1B function is associated with microtubule and actin microfilament polymerization and dynamics. In recent years, the generation of molecular models to inactivate MAP1B function in invertebrates and mammals has sparked some controversy about the real role of MAP1B. Despite discrepancies between some studies, it is clear that MAP1B plays a principal role in the development of the nervous system. In this article, we summarize the evidence for MAP1B function in a wide variety of cellular processes implicated in the proper construction of the nervous system. We also discuss the role of MAP1B in pathological processes.